The airport will be without a licence until 19 December
All flights in and out of Newquay have been cancelled for three weeks from Sunday because of a problem over air traffic support.
Cornwall County Council, which owns Newquay Airport, had been due to take over air traffic operations from the RAF on 1 December.
But the council said there was a delay in securing a Civil Aviation Authority (CAA) licence until 19 December.
Some flights will be rescheduled to fly from other South West airports.
An estimated 460,000 passengers are due to pass through Newquay Airport this year.
An MoD spokesman said: "The MoD is to vacate the airfield on 1 December in accordance with our agreement with Newquay Cornwall Airport.
"We regret that we have not been able to agree to the request to extend our support to the airport, this is because the RAF personnel who are employed at the airfield are required for operational posts elsewhere."
The RAF decision not to continue providing air traffic cover means the airport is effectively without a licence until 19 December.
Andrew Mitchell, from Cornwall County Council, said: "We are very sorry for the inconvenience this temporary cancellation of flights from the airport will cause to those who have booked flights during this period.
"We are clearly very disappointed that the RAF has not been able to continue to operate the airfield beyond 1 December.
"We would like to place on record our sincere appreciation for the cooperation we have received from the RAF throughout this project."
Passengers have been advised to contact their airline.
Air Southwest has said it will try to reschedule flights to fly from Plymouth airport, while Skybus, which flies to the Isles of Scilly, will use a facility at Lands End.
Cornwall County Council said flights up to 30 November will not be affected.
The RAF has provided air traffic control support for Newquay airport until now because the RAF St Mawgan airbase is next door.
But the base has been scheduled for closure for some time and Cornwall County Council has been in negotiation with the MoD to buy the site with a view to expanding the airport.