Civil Aviation Authority chair Janice Fredric apologised for the failures in a statement released today by Transport Minister Phil Twyford.
A report into management at the CAA has also been released.
The review found that bad behaviour was able to occur within the CAA because of failures of leadership to identify and address issues including bullying and sexual harassment.
However, the report found no evidence of a deliberate and tolerated culture of bullying and harassment.
The review included more than 100 confidential interviews with past and present staff members.
A separate review into inappropriate conduct within the aviation security service, Avsec, is still under way.
Twyford said the report found "a poor approach to managing employee well-being and ensuring a healthy culture".
"This includes instances where allegations of bullying and harassment were not appropriately addressed."
CAA chief executive Graeme Harris retired this month, although the Ministry of Transport would not be drawn on whether Harris' retirement was related to the review into the authority's culture
The previous chair, Nigel Gould, also resigned last year following a request from the Government.
The Public Service Association said the review into CAA management made for "tough reading".
The union said it took "sustained pressure from whistleblowers, media and unions before awareness of this toxic culture reached high enough in government for action to be taken, and a long process of reform lies ahead".
PSA national secretary Glenn Barclay said the PSA's submission to the Ministerial Review had pointed out that "not only have bullying and harassment been long standing problems, whistleblowers who challenged this were treated badly".
