RAF Kinloss is set to close after ministers cancelled orders for the new Nimrod as part of the UK government's defence review.
Nine of the MRA4 surveillance aircraft were due to be based in Moray.
RAF Kinloss station commander Group Captain James Johnston said there had been disbelief when the announcement was made.
The future of nearby RAF Lossiemouth, home to Tornado squadrons, remains uncertain.
However, there was better news for shipbuilding in Govan and Rosyth, with orders for two new aircraft carriers going ahead.
Prime Minister David Cameron said that as a result of the cancellation of the Nimrod replacement, RAF Kinloss would no longer be required.
It is understood that the Ministry of Defence could retain the site and may eventually use it as a barracks for soldiers returning from Germany.
Defence sources say the troops would not arrive until about 2015 at the earliest.
A final decision has not yet been taken about RAF Lossiemouth.
It has been feared that the Tornado aircraft currently based at RAF Lossiemouth could be transferred to RAF Marham.
Deputy Prime Minister Nick Clegg said: "Cancelling the Nimrod aircraft of course has a knock-on effect on the bases in Moray, but it's not the end of the story.
"We're not going to abandon the families and communities which are dependent for their jobs and their livelihoods on those bases."
Moray's two RAF bases contribute more than £150m to the local economy annually and support 5,700 jobs, according to a report in August by consultants hired by Highlands and Islands Enterprise (HIE).
Staff at Kinloss and Lossiemouth were briefed on developments after the prime minister's statement.
Despite the major cuts, the coalition government formally confirmed that it is going ahead with the order for the two new aircraft carriers.
The decision will safeguard thousands of jobs on the Clyde and the Forth.
Mr Clegg said: "The workers are delighted to have heard we have now confirmed that the two aircraft carriers will go ahead because that means their jobs and skills are being safeguarded for the future."
Angus Robertson MP, the SNP's Westminster leader, said: "The Ministry of Defence should retain both RAF Kinloss and RAF Lossiemouth, and it also has a responsibility to be clear to the Moray community and service families about their plans.
"The importance of both bases to the local economy and society is massive.
"Should they close it is the equivalent to 700,000 job losses in Greater London."
RAF Leuchars in Fife is also set to continue.
MoD sources said no Scottish infantry battalions would be cut in the defence review and that the Royal Marine base at Condor in Arbroath was also unaffected.
However, BBC Scotland understands that there will be a restructuring of army command which will see the axing of 2nd Division - the army's command for Scotland, Northern Ireland and the north of England, based in Edinburgh.
It is thought army command will be centralised elsewhere, but government sources said that the HQ in Edinburgh would remain open.
'Heart and soul'
Labour's shadow defence secretary, Jim Murphy, said: "This is mixed news for Scotland. It is great that the government isn't going to sink the carriers, but their plans are bizarre.
"It is eccentric to have aircraft carriers with no aircraft flying off them for another decade.
"People at home are scratching their heads - and so are defence experts.
"The report is a body blow to Kinloss and people in Moray."
Bob Rollings, MoD group secretary for the Public and Commercial Services union, said: "David Cameron is callously using his 'admiration' for our armed forces as a spiteful tool to attack public services.
"The public will not be fooled into believing that cuts have to be made when there are uncollected taxes in excess of £120bn."