The plan has angered people leaving nearby who have launched legal action to block the move, which they say will endanger lives due to the possibility of accidents and the prospect that aircraft could be shot down over densely populated areas.
"This is the biggest sporting event in the world, and with that comes the huge responsibility to deliver it safely and securely," interior minister Theresa May said of the Olympic Games, which begin on July 27, Reuters reports.
The anti-aircraft missile systems - one large and mounted on a trailer, the other handheld - will be deployed at six locations around the Olympic Park in the east of the capital, including on top of two residential buildings and in parkland.
The Stop the Olympic Missiles campaign says the plan will turn the games into a "festival of the global security industry", according to the group's website.
"The government is ignoring public opinion," said campaigner Chris Nineham.
"The vast majority of people in east London do not want these missiles. The government decision flies in the face of good sense and our campaign will go on," he told Reuters.
Britain's defence ministry said it acknowledged that the defence system would have "implications" for those on the ground, but that missile deployment would be a "last resort option" to minimise casualties and damage from an aerial attack.
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