The airport will be without a licence until 19 December
Ryanair has described Cornwall County Council as "Keystone Cops" over its handling of Newquay Airport and has cancelled its services from 1 December.
All airlines' flights have been stopped for three weeks in December because of a delay in gaining an aviation licence.
Ryanair said the situation had "descended into farce".
Cornwall County Council, which owns the airport, had been due to take over air traffic operations from the RAF on 1 December.
But as the Civil Aviation Authority did not grant it a licence it has had to cancel all flights in and out until 19 December.
An estimated 460,000 passengers were due to pass through the airport this year.
Ryanair spokesman Stephen McNamara said: "It is simply unacceptable that Ryanair and its passengers are given just four days notice of the closure of Newquay Airport for the month of December.
"We will now have to contact thousands of passengers over the coming days - many of whom will be abroad and will be unable to travel back to Newquay - and tell them that the airport has been closed due to the incompetence of Cornwall County Council and the unwillingness of the RAF to keep the airport open for a couple of weeks."
Ryanair said it had "no alternative" other than to cancel all Newquay flights from December "until further notice".
The airline added that it did not think it was unreasonable to expect the RAF to keep Newquay open for another three or four weeks to avoid the disruption.
The MoD said it had planned to vacate the airfield on 1 December in accordance with its agreement with the airport.
It said that it "regretted" not being able to extend its support, but that the RAF personnel employed at the airfield were required for operational posts elsewhere.
It said: "We will work hard across government and with the county council to ensure we minimise the impact on the airport and the region."
Cornwall County Council said contingency plans were in place - adding that flights up to 30 November would not be affected and that some flights would be rescheduled to fly from other South West airports.
Air Southwest has reassured customers that all its flights due to operate from Newquay from December 1 to 19 inclusive will now be routed through Plymouth with transport laid on to ferry passengers between the two sites.
The councillor responsible for the Newquay Airport project, Andrew Mitchell, said that the situation was "very disappointing".
He said: "We need to see what has gone wrong.
"We were hoping to have a smooth transition from military to civilian, but there are obviously some logistical and contractual issues that need to be sorted out."
Passengers have been advised to contact their airline.
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.