The Exeter-based airline has informed the stock market that Andrew Strong, the managing director of Flybe UK, Mike Rutter, the managing director of Flybe Outsourcing Solutions, and Mark Chown, director of corporate strategy, all left their positions on Friday.
Flybe UK and Flybe Outsourcing Solutions have been disbanded and their operations rolled into the single unit.
The shake-up comes after chief executive Saad Hammad ordered a full review of Flybe's operations after replacing Jim French in August. Mr Hammad said: "It has become clear to me that Flybe's prospects will be significantly enhanced by disbanding the existing divisional structure and integrating all operations into a single, simpler and lower cost operating unit.
"Today's announcement facilitates that move and will inform an important part of the strategic review of the business, which I expect to conclude in November."
Flybe previously announced that Paul Simmons would join as chief commercial officer on October 28. It said Matt Bennett, currently director of internal audit and risk, will act as director of special projects in addition to his current duties, with current director of aircraft maintenance John Palmer becoming interim director of operations until the role is filled.
In January Flybe embarked on a two-year recovery plan under which it is aiming to make £40 million in cost savings by the end of this year, rising to £50m by 2014/15.
It is aiming to reduce its workforce by 21% or 580 out of the 2730 UK-based jobs it employed in February.
Shares in Flybe closed unchanged at 89p.