Philip Hammond said he was prepared to make the dramatic order if necessary even if the jet was packed with innocent passengers.
Mr Hammond also dismissed suggestions he was going “over the top” after the Royal Navy’s largest warship was sailed up the River Thames as part of an Olympics security exercise.
The build up of security plans for the summer games has fuelled concerns among some London residents after they discovered plans to site ground to air missiles launchers in their area.
Six sites have been confirmed by the Ministry of Defence, including two on the roof of residential flats.
Asked if he was prepared to act to prevent a 9/11 style attack during the Olympics, Mr Hammond said: “Of course, I’m certainly prepared to make decisions.”
He added: “We rehearse these things. All the ministers involved are fully versed in the processes they have to go through, the judgments they have to make.”
The Defence Secretary also sought to reassure residents over the missile launcher sites, adding they should be “reassured by the military presence”.
“We are not talking about a war with an enemy trying to take out our air defences. These defensive sites are not going to be targets.”
He also warned against protesters not to engage in “stupid stunts” such as the recent disruption of the Boat Race.
HMS Ocean berthed at Greenwich in east London ahead of a major security exercise named Olympic Guardian.
The ship will act as a launch pad for eight Lynx helicopters and a base for Royal Marine snipers.
Mr Hammond, who was taken on board by a landing craft, said: "I don't think it's over the top.
"Every Olympic Games in recent times has had a significant military component to its security plan."
General Sir Nick Parker, in charge of the military's Olympics role, said the security exercise would prepare for the possibility of "extreme threats".
"One would want the world to know that we are taking security for the Olympics seriously,” he said.
• Extra commercial flights could be allowed at RAF Northolt to help fund the cost of the airbase, Mr Hammond said.
"Northolt is a very important RAF facility close to London," he said.
"There is scope for some limited additional use for business jets in order to make it viable as a continued RAF facility."
He added: “We rehearse these things. All the ministers involved are fully versed in the processes they have to go through, the judgments they have to make.”
The Defence Secretary also sought to reassure residents over the missile launcher sites, adding they should be “reassured by the military presence”.
“We are not talking about a war with an enemy trying to take out our air defences. These defensive sites are not going to be targets.”
He also warned against protesters not to engage in “stupid stunts” such as the recent disruption of the Boat Race.
HMS Ocean berthed at Greenwich in east London ahead of a major security exercise named Olympic Guardian.
The ship will act as a launch pad for eight Lynx helicopters and a base for Royal Marine snipers.
Mr Hammond, who was taken on board by a landing craft, said: "I don't think it's over the top.
"Every Olympic Games in recent times has had a significant military component to its security plan."
General Sir Nick Parker, in charge of the military's Olympics role, said the security exercise would prepare for the possibility of "extreme threats".
"One would want the world to know that we are taking security for the Olympics seriously,” he said.
• Extra commercial flights could be allowed at RAF Northolt to help fund the cost of the airbase, Mr Hammond said.
"Northolt is a very important RAF facility close to London," he said.
"There is scope for some limited additional use for business jets in order to make it viable as a continued RAF facility."
http://www.telegraph.co.uk/news/uknews/defence/9246292/I-will-shoot-down-rogue-aircraft-during-Olympics-vows-Defence-Secretary.html
