Malcolm Carroll, a Plane Stupid spokesman, said: "This is all about no third runway. The direct action movement know we have got to take these protests to another level to get the government to listen."
Security at the Houses of Parliament was increased after the September 11, 2001, attacks in the United States.
It was further tightened when fathers' rights protesters hurled coloured flour at Tony Blair, the then prime minister, in May 2004 while he was in the debating chamber.
The government, business groups, airlines and British Airports Authority, the UK's main airport owner, say Heathrow must either expand or risk losing out to continental rivals serving emerging destinations in India and China and damaging the economy.
However, environmental groups have joined forces with angry local residents, saying roughly doubling the number of flights from the airport would make a mockery of government pledges to reduce carbon emissions to tackle global warming.
Speaking in parliament, as the protest continued above his head, Gordon Brown, the British prime minister, said: "Decisions in this country should be made in the chamber of this house and not on the roof of this house."
The campaigners, who were escorted down from the roof by police just before 1230 GMT after a protest lasting two hours, say the Heathrow consultation was a sham and have pinned their hopes on the government being swayed by public pressure.
Residents' groups, also furious over increased noise pollution and the demolition of 700 homes around the airport, say they are preparing court action and if necessary will try to block the bulldozers if expansion goes ahead.
They are supported by Ken Livingstone, London's mayor, a string of local councils and the Liberal Democrats, Britain's third-largest political party.
Heathrow already handles 67.3 million passengers and 471,000 aircraft movements a year.