Six members of the group called Plane Stupid unfurled two huge banners and threw paper airplanes while police tried to talk them into coming down, The Times of London reported.
The demonstrators indicated they planned to stay until midday when the prime minister's questions session was due to begin.
British Prime Minister Gordon Brown addressed the protest, saying, decisions must be made "in the chamber of this House (of Commons) and not on the roof of this House," the BBC reported.
When asked why police didn't force them down, one source told The Times that some of the protesters appeared to have chained themselves to the railings.
Police said there was a strong possibility the demonstrators gained access to the building as guests of pass-holders.
It was the second security breach this week caused by those opposed to adding a third runway to Heathrow. On Monday five Greenpeace activists climbed on top of a British Airways plane that had just landed at the airport.