WASHINGTON (Reuters) -The head of the Federal Aviation Administration who has overseen the agency's response to significant safety issues at Boeing since a mid-air emergency in January will step down on Jan. 20, the agency said on Thursday.

FAA Administrator Mike Whitaker, who was confirmed to a five-year term in October 2023, will depart when President-elect Donald Trump takes office. The FAA also said Deputy Administrator Katie Thomson will step down on Jan. 10, which will mean Mark House, the agency's assistant administrator for finance and management, will be the agency's senior acting official during the transition.

SpaceX CEO Elon Musk, a close adviser to Trump, in September called for Whitaker's resignation and harshly criticized the FAA's proposed $633,000 fine to SpaceX after the agency said it violated launch license requirements.

Trump has said he plans to oust many officials before their terms expire.

Last week, Whitaker told Reuters he was unsure if he would stay beyond Jan. 20 as conversations with the transition team continued.

"As I conclude my time at the FAA, my confidence in you to meet our safety mission has never been stronger," Whitaker said in a memo to employees on Thursday.

Whitaker's tenure has been consumed with addressing Boeing safety issues after a door panel missing four key bolts flew off an Alaska Airlines 737 MAX 9 at 16,000 feet.

He took the unprecedented step of capping production at 38 737 MAX planes per month in January and has insisted Boeing make dramatic safety improvements before he would restore authority.

Whitaker, who announced another audit of Boeing in October, has said it could take five years for Boeing to reform its safety culture, but noted the planemaker has deployed a new parts management system and improved training.

He has also dealt with continuing air traffic control staffing issues and a series of near-miss incidents that have raised safety concerns.