Military snipers are to be deployed in helicopters during the London Olympics and if required will shoot pilots of low-flying aircraft that might be involved in terrorist attacks, it emerged on Monday.

A team of seven snipers is being given "comprehensive on-the-ground and in-the-air training" as part of the all encompassing security operation being undertaken by the police and the army.

General Sir Nick Parker, who is in charge of co-ordinating the armed forces during the 2012 Games, described the role of the snipers as he revealed the six sites where anti-aircraft missiles may be based as part of the security operation.

The four that are in open spaces – at Blackheath, Lea Valley reservoir, Shooters Hill and Epping Forest – will be home to a battery of Rapier surface-to-air missiles, which are the UK's primary air defence weapon.

Smaller high-velocity missiles (HVMs) will be put on the top of residential buildings in Tower Hamlets and Waltham Forest.

Parker said the missiles would only be fired as a "very last resort", and any decision to use them would have to come from the "very highest level" – on the authority of the prime minister.

At a briefing at Scotland Yard with assistant commissioner Chris Allison, Parker said it was right to plan for worst-case scenarios, and identified two "broad airborne threats" the military could help with.

"The focus is on the air security of the Olympic Park. The two threats are a large 9/11 type of threat which is integrated into existing security plans. Then there is the smaller, what we would describe as the 'low and slow', that is particularly what we need to practice over London."

Parker said RAF Typhoon fighters and the anti-aircraft missile systems would help to deter the larger threats, and the snipers would be used for the smaller ones. The marksmen will be used in rotation from four Lynx helicopters based on HMS Ocean, which will be in the river Thames at Greenwich, and three Puma helicopters based at a territorial army headquarters in Ilford.

"We put snipers into the helicopters … they won't all be flying at the same time. It is a standby capability and you operate one sniper in each aircraft. This is part of our layered response. The very final thing would be to shoot the pilot and we are conducting some comprehensive training on the ground and in the air so these snipers can do their job."

That training will come into focus on Wednesday, when the police and armed forces begin an eight-day exercise in London and Weymouth. This will include Typhoons and helicopters flying low over the capital so the military can "test their ability to the limit", said Parker. The final decision about if and where to deploy the anti-aircraft missiles will be taken following the exercise.

Allison would not say how many British police would be armed during the Games, but said the "vast majority" would not be carrying weapons. He also insisted that no diplomatic or security officials from other countries, including the US, would be carrying firearms during the event.

"The planning assumption is that there will be no other armed officers from across the world," he said. "The Games will be policed by the British police … if there are any firearms required, it will be the British police who will be using their firearms."

Allison said the police would not try to stop legitimate and peaceful protests during the Olympics. But he said that did not give people "the right to stop the Olympics happening, or the right to stop the torch bearer from having a once in a lifetime opportunity, or the right to stop an athlete who has trained for years and years for their one chance of a gold medal".

In all, 51 different police forces are now sending officers to support Olympic security; 12,500 police will be involved in the Games, and 13,500 members or the armed forces. Parker said he hoped most people regarded the military as a "very benign presence".