The crash into the Java Sea after take-off from Jakarta, which killed all 62 people on board, was Indonesia's third major commercial plane crash in just over six years and shone a spotlight on its poor air safety record.
A working autothrottle is not required for a plane to be dispatched because pilots can control the thrust levers manually.
The first officer said "upset, upset" and "captain, captain" before the recording stopped, but the captain's channel was not working, making it more difficult for investigators to analyse events.
KNKT had raised the lack of upset recovery training after the 2014 crash of an AirAsia Indonesia jet that killed all 162 people on board.
Indonesia is putting in place updated upset prevention and recovery training, KNKT said in the report.