Narrative:

I filed an IFR flight plan to depart from luis munoz marin international airport; san juan pr (sju) to another airport in the virgin islands on a far part 135 flight. Thirty minutes prior to departure we received the departure clearance as follows: san juan cleared us via radar vectors direct destination; climb and maintain 6;000 ft; squawk XXXX; departure frequency on 120.9. My first officer read the clearance back to clearance delivery and was told 'read-back correct' the avionics and FMS were set up with our filed route. 6;000 ft was entered into the altitude pre-selector and all pre start checklist were completed. After engine start; taxi; and pre-departure route brief; we were lining up number 2 behind a B737 at the hold short line of taxiway S1 at active runway 8. We changed over to the tower frequency. When the B737 was cleared for takeoff; we were issued a clearance to 'line up and wait on runway 8; caution for jet blast!' now we are lined up and waiting with our backs to the approaching landing traffic. After about 15-20 seconds we are cleared for takeoff with a turn to 060 degrees; my first officer reads the clearance back and we departed. At this point neither my first officer nor I can recall if an altitude change was issued in the takeoff clearance. We were both expecting to climb to 6;000 ft. If the initial clearance was changed to 5;000 ft in our line up and wait takeoff clearance; I did not hear hit nor was it changed in our altitude pre-selector or FMS. We were climbing to 6;000 ft. After takeoff and climbing through approximately 4;000 ft it had appeared sju tower had forgotten about us. My first officer queried the tower as to whether they wanted us to contact departure control. The tower immediately replied back 'contact san juan departure.' my first officer checked on with san juan departure and reported our present altitude and climbing to 6;000 ft on a 060-degree heading assigned. The controller responded back with 'roger; radar contact'. Shortly after that; departure issued a clearance 'turn right to 150 degrees and expect to join the filed routing.' I rotated the heading bug right; to 150 degrees and the autopilot turned the airplane to 150 heading. I did not select the navigation function on the autopilot to join the route yet because I was not cleared to join. During this time a few radio calls were made to the departure controller from another aircraft and she would reply back to them but use our n- number. Each time we would reply back to her that she was responding to the wrong aircraft n-number. After completing the turn to 150 degrees we were just about to level off at 6;000 ft MSL. We had already noticed a target on the TCAS at 6;000 ft as well. We were in VMC and had visual contact with traffic off to our right and were able to maintain separation with the traffic. Then we got a TA on the TCAS and at the same time were issued a clearance to climb to 9;000 ft. My first officer reads back the clearance and sets 9;000 ft in the altitude pre-selector and I began to climb to 9;000 ft from 6;000 ft. At 6;200 ft the controller asked us to verify our present altitude is 6;200 ft. My first officer responded back '6;300 ft climbing to 9;000 ft.' then she told us to copy down a phone number and to call when we landed. No flight path deviation was needed for the TA. If we were already at the wrong altitude; why would ATC turn us into conflicting traffic? We could have resolved the altitude misunderstanding on the earlier 060 assigned heading. We told ATC that we were climbing to 6;000 ft. Why turn us toward traffic that is already at 6;000 ft? By this time we were flying through the expected route course with no clearance to join. Then we were handed off to the next san juan controller. My first officer checked on with the next san juan controller and stated that we were climbing to 9;000 ft heading 150 degrees assigned. The controller questioned our assigned routing and told us that we were supposed to have joined the routing and that we were already through the course. We were never cleared to join the route. She continued to give us vectors until handing us off to our destination tower. The rest of the flight was uneventful. After landing; I called the number we were given. I was told that I had violated an altitude clearance to climb and maintain 5;000 ft after departure from sju. My first officer and I cannot recall ever being issued a clearance to climb to 5;000 ft as apposed to 6;000 ft. If we were issued a clearance to climb to 5;000 ft while lined up and waiting on an active runway with landing traffic behind us; I could see how this could be missed on the radio. I feel that when a 'line up and wait' clearance is issued this is not the time to be issuing new or different change to the planned departure course. Before take-off; that would be fine. We would have time to change altitude selectors and FMS data; however to be in position and holding; ready to release the brakes and run down the runway is no time for my right seater to be rotating dials and plugging information into the FMS. He/she will be busy managing the cockpit on the take off roll. I know it doesn't take long to plug some info into the FMS or altitude selector; but how long is too long to sit on a runway with my back turned to the landing traffic and receive a change to my departure clearance during my take off clearance? When tower clears you to take off; they are expecting you to begin you take-off roll immediately unless you need to abort. If we were issued a clearance and we did not adhere to it; then why when we checked on with the departure controller and reported climbing to 6;000 ft were we not told at that time that was not our assigned altitude? Why we were not told at that point that we were climbing to an incorrect altitude; we were certain that we were supposed to climb to 6;000 ft no questions asked? If the clearance was changed on the takeoff roll; then I as the pilot in command of this aircraft take full responsibility for not catching this mistake. I do feel however that during a 'line up and wait clearance' this is an unsafe time to be changing clearances.

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Original NASA ASRS Text

Title: A pilot reported that after departing SJU and leveling at 6;000 FT the two person crew was notified that they were earlier only cleared to 5;000 FT. Neither pilot heard a revised altitude prior to takeoff or in flight.

Narrative: I filed an IFR Flight Plan to depart from Luis Munoz Marin International Airport; San Juan PR (SJU) to another airport in the Virgin Islands on a FAR Part 135 flight. Thirty minutes prior to departure we received the departure clearance as follows: San Juan cleared us via radar vectors direct destination; climb and maintain 6;000 FT; squawk XXXX; departure frequency on 120.9. My First Officer read the clearance back to Clearance Delivery and was told 'read-back correct' The Avionics and FMS were set up with our filed route. 6;000 FT was entered into the Altitude Pre-selector and all Pre Start Checklist were completed. After engine start; taxi; and pre-departure route brief; we were lining up number 2 behind a B737 at the hold short line of Taxiway S1 at active Runway 8. We changed over to the Tower frequency. When the B737 was cleared for takeoff; we were issued a clearance to 'line up and wait on Runway 8; caution for jet blast!' Now we are lined up and waiting with our backs to the approaching landing traffic. After about 15-20 seconds we are cleared for takeoff with a turn to 060 degrees; my First Officer reads the clearance back and we departed. At this point neither my First Officer nor I can recall if an altitude change was issued in the takeoff clearance. We were both expecting to climb to 6;000 FT. If the initial clearance was changed to 5;000 FT in our line up and wait takeoff clearance; I did not hear hit nor was it changed in our Altitude Pre-selector or FMS. We were climbing to 6;000 FT. After takeoff and climbing through approximately 4;000 FT it had appeared SJU Tower had forgotten about us. My First Officer queried the Tower as to whether they wanted us to contact Departure Control. The Tower immediately replied back 'Contact San Juan Departure.' My First Officer checked on with San Juan Departure and reported our present altitude and climbing to 6;000 FT on a 060-degree heading assigned. The Controller responded back with 'Roger; RADAR contact'. Shortly after that; Departure issued a clearance 'Turn Right to 150 degrees and expect to join the filed routing.' I rotated the heading bug right; to 150 degrees and the autopilot turned the airplane to 150 heading. I did not select the NAV function on the autopilot to join the route yet because I was not cleared to join. During this time a few radio calls were made to the Departure Controller from another aircraft and she would reply back to them but use our N- number. Each time we would reply back to her that she was responding to the wrong aircraft N-number. After completing the turn to 150 degrees we were just about to level off at 6;000 FT MSL. We had already noticed a target on the TCAS at 6;000 FT as well. We were in VMC and had visual contact with traffic off to our right and were able to maintain separation with the traffic. Then we got a TA on the TCAS and at the same time were issued a clearance to climb to 9;000 FT. My First Officer reads back the clearance and sets 9;000 FT in the altitude pre-selector and I began to climb to 9;000 FT from 6;000 FT. At 6;200 FT the Controller asked us to verify our present altitude is 6;200 FT. My First Officer responded back '6;300 FT climbing to 9;000 FT.' Then she told us to copy down a phone number and to call when we landed. No flight path deviation was needed for the TA. If we were already at the wrong altitude; why would ATC turn us into conflicting traffic? We could have resolved the altitude misunderstanding on the earlier 060 assigned heading. We told ATC that we were climbing to 6;000 FT. Why turn us toward traffic that is already at 6;000 FT? By this time we were flying through the expected route course with no clearance to join. Then we were handed off to the next San Juan Controller. My First Officer checked on with the next San Juan Controller and stated that we were climbing to 9;000 FT heading 150 degrees assigned. The Controller questioned our assigned routing and told us that we were supposed to have joined the routing and that we were already through the course. We were never cleared to join the route. She continued to give us vectors until handing us off to our destination Tower. The rest of the flight was uneventful. After landing; I called the number we were given. I was told that I had violated an altitude clearance to climb and maintain 5;000 FT after departure from SJU. My First Officer and I cannot recall ever being issued a clearance to climb to 5;000 FT as apposed to 6;000 FT. If we were issued a clearance to climb to 5;000 FT while lined up and waiting on an active runway with landing traffic behind us; I could see how this could be missed on the radio. I feel that when a 'Line Up and Wait' clearance is issued this is not the time to be issuing new or different change to the planned departure course. Before take-off; that would be fine. We would have time to change altitude selectors and FMS data; however to be in position and holding; ready to release the brakes and run down the runway is no time for my right seater to be rotating dials and plugging information into the FMS. He/She will be busy managing the cockpit on the take off roll. I know it doesn't take long to plug some info into the FMS or altitude selector; but how long is too long to sit on a runway with my back turned to the landing traffic and receive a change to my departure clearance during my take off clearance? When Tower clears you to take off; they are expecting you to begin you take-off roll immediately unless you need to abort. If we were issued a clearance and we did not adhere to it; then why when we checked on with the Departure Controller and reported climbing to 6;000 FT were we not told at that time that was not our assigned altitude? Why we were not told at that point that we were climbing to an incorrect altitude; we were certain that we were supposed to climb to 6;000 FT no questions asked? If the clearance was changed on the takeoff roll; then I as the pilot in command of this aircraft take full responsibility for not catching this mistake. I do feel however that during a 'line up and wait clearance' this is an unsafe time to be changing clearances.

Data retrieved from NASA's ASRS site as of April 2012 and automatically converted to unabbreviated mixed upper/lowercase text. This report is for informational purposes with no guarantee of accuracy. See NASA's ASRS site for official report.