Bailey joined the department in 2006, having previously worked in the press offices of the Department for Health and the Home Office.
He is understood to have taken voluntary redundancy. No decision has been made about a replacement.
The details of Bailey's departure come just weeks after the arrival of James Frayne as the department's director of comms. Frayne took the top comms role in March, having previously worked for public affairs firms Westbourne and Portland.
However, Bailey stressed that his decision to take voluntary redundancy was in no way linked to Frayne's arrival.
In a statement, Frayne said: 'Lee has been one of the stars of government communications for more than a decade and we're sorry to see him go. Lee is obviously going to be in demand from a range of organisations. You don't get many people of his calibre coming on to the market in a typical year.'
The former permanent secretary for comms Matt Tee also commended the departing Bailey, describing him as 'one of the best media handlers I have worked with'.