The environmentalists, three men and two women, who spent three hours on the roof before leaving during a traditional session of Prime Minister's Question time, were arrested by police. They said the airport expansion would inevitably lead to an increase in greenhouse gas emissions and could speed up global warming.
One of the demonstrators, Richard George, 27, said while on the roof: "This prime minister doesn't even have the courage to ask Londoners the very simple question, do you want a third runway? Instead his government published a consultation document full of gobbledygook and industry spin."
The protestors, concerned by increased noise levels if the runway project goes ahead, unfolded banners saying "No Third Runway" and "BAA HQ" accusing the government of colluding with the aviation industry.
They also threw paper planes from the roof, a move which was popular with the numerous tourists who took photos of the scene.
The environmentalists are believed to have breached parliament's security disguised as MPs' visitors and then made it onto the rooftop. Police said they are conducting an investigation into the breach.
Gordon Brown condemned the protest. "Decisions in this country should be made in the chamber of this house and not on the roof of this house," he told MPs.
The rooftop demonstration comes two days after activists from Greenpeace penetrated security at Heathrow Airport, climbing on top of a British Airway's plane and unfurling a banner.
London Heathrow Airport is the biggest airport in Europe and, with over 67 million passengers a year, is one of the world's busiest.
