Speaking at RAF Northolt in north-west London, Air Vice-Marshal Stuart Atha said a plane could be shot down as a last resort in a “worst-case scenario”.
Asked who would give the order, he said: “The highest level of government makes that decision.”
A series of airspace restrictions around London and south-east England are set to be enforced after midnight.
Typhoon jets and Sea King helicopters are being deployed to RAF Northolt.
The prohibited zone will be about 30 miles wide and does not affect commercial aircraft, which fly in established air traffic corridors.
The temporary additional restrictions to airspace in and around the capital come into force at 00:01 BST on Saturday and will last for a month.
Also on Friday, the Prime Minister David Cameron said: “I’m absolutely clear that if companies don’t deliver on their contracts then they should be pursued for that money”.
His comments came after security firm G4S admitted it might not be able to provide enough guards for the Olympics and 3,500 extra military personnel would be needed.
But Mr Cameron tried to change the focus of attention away from security, saying: “We should be raising our sights, and thinking of the incredible inspiration that these Games are going to bring.
“The facilities are built, the country is ready, we are in really good shape.”
But Ian Swales, a Liberal Democrat MP, said G4S should have provided a “Rolls-Royce service” after increasing its charges by £198m.
Mr Swales, a member of the public accounts committee who scrutinised some of the Olympic contracts, told the BBC Radio 4′s World At One : “We were really concerned because when the announcement of doubling of the number of security personnel was made we looked at the breakdown of the costs and we saw that the G4S contract was going up from £86m to £284m, which felt like a colossal amount of money.”
The Home Affairs Select Committee has summoned G4S chief executive Nick Buckles to appear before them on Tuesday to explain what has gone wrong with the Olympics security contract.
Keith Vaz, the committee’s chairman, said: “G4S has let the country down and we have literally had to send in the troops.”
Shadow home secretary Yvette Cooper said the situation looked like “another Home Office shambles”.
G4S admitted it was experiencing “some issues in relation to workforce supply and scheduling”. A spokesman added: “This has been an unprecedented and very complex security recruitment, training and deployment exercise which has been carried out to a tight timescale.”
A Home Office spokesman said: “We are planning on a terrorist threat environment that is severe… we are not suggesting that there is any particular threat or risk to the Games that we know about.”
Details have been released about how the Typhoons and Sea Kings would act if they intercepted an aircraft.
A suspicious aircraft would be contacted by radio and ordered to rock its wings to acknowledge the warning, follow the military aircraft and turn away from London.
Flares and lasers could be fired by the military aircraft and, as a last resort, if an aircraft failed to comply with the directions of the military aircraft, it may be considered to be a threat to security, which may result in the use of lethal force.
HMS Ocean is also set to return to London with a deployment of Royal Marines to provide security on the River Thames.
It comes the day after ground-based air defence systems were installed at four sites in and around London.
Earlier this week, Typhoon fighters were deployed to RAF Northolt, while RAF Puma helicopters and snipers were deployed to Ilford in east London.
The Civil Aviation Authority (CAA), National Air Traffic Services (Nats) and the MoD have worked together to inform pilots about the restrictions and how people can continue to use the UK’s airspace during the Olympics.
BBC news correspondent Nick Childs, at RAF Northolt, said: “This is very much a last-minute information offensive by the authorities to make sure that every pilot in the UK knows that these restrictions are coming into effect from midnight tonight.
“The message is that it should not affect in any way scheduled airlines but it will affect general aviation and pilots in particular.”
He said pilots of light aircraft could still fly over London, but only if they had gone through a series of security procedures.