Civil Aviation Authority (CAA) chairperson Nigel Gould has resigned following a request from the government.
Transport Minister Phil Twyford said on Wednesday evening: "I told Mr Gould the CAA was going through some big changes and it would be best to have fresh leadership at this time. I have thanked him for his service to the authority."
Mr Gould told Checkpoint Mr Twyford gave him no other reasons for wanting him to step down from the position.
The pair had the conversation on Tuesday, which, Mr Gould said, had come as a surprise given his contract had been extended by another 12 months in June.
"I'm obviously disappointed. My term should have finished in June and at his request I agreed to stay on for another 12 months," he said.
"There are a lot of things going on ... at the moment and ... I was prepared to make the time available and contribute to that, a lot of things that potentially have a very wide impact."
He said he could not make any comment about Mr Twyford's motivations.
Mr Gould's resignation followed recent claims that the body was a toxic workplace, where bullying and sexual harassment had been tolerated.
In June this year, the Civil Aviation Authority was under scrutiny amid reports of high staff turnover and a culture of bullying.
Then in August, the CAA was accused of misleading the public about the number of helicopter inspectors on its staff when a fatal crash killed seven people in 2015.
There would be transition period before Mr Gould's association with the CAA ended.