Queues grew and tempers frayed in the departure lounge at Stansted Airport after budget airline Ryanair cancelled 56 flights as a result of the early-morning protest by Plane Stupid.
Activists broke into a secure area at around 3am, forcing the runway to remain closed for three hours.
Ryanair called for an investigation into why airport operator BAA had failed to keep the Essex airport "secure and open", saying the disruption to passengers was "unacceptable".
Travellers caught up in the queues for information expressed little sympathy for Plane Stupid's stance that disruption would prevent "the release of thousands of tonnes of greenhouse gas emissions into the atmosphere".
Lainey Mace, of Fakenham, Norfolk, said: "They have caused great inconvenience."
She added: "It is very worrying that protesters were able to get either close to the runway or on the runway.
"One would have thought security at an airport would be much tighter than that."
Today's protest was sparked by the Government's decision to allow the expansion of the airport with a second runway.
Activist Lily Kember, 21, a third-year anthropology student at Edinburgh University, said the group used bolt-cutters to get into a secure area around 55 yards (50m) from the runway.
Ms Kember, from London, said: "Being arrested is a terrifying prospect, but not nearly as terrifying as the threat of climate change."
BAA said protesters did not get on to the runway, but it was closed as a "precaution".
The runway had been due to open at 5am after maintenance work but remained closed until 8.10am, causing delays to flights in and out of Stansted.
Ryanair, the only airline to cancel flights, said: "Ryanair will be calling for an investigation as to why the BAA Stansted security has once again failed to keep Stansted Airport secure and open to the travelling public.
"It is unacceptable that the travel plans of thousands of passengers have been disrupted because BAA Stansted security have failed to remove a number of protesters."
Long queues formed at Ryanair check-in desks and armed police officers helped to keep order as a small number of passengers became irate.
Airline staff were forced to shout in an attempt to get passengers on planes, at one point yelling "Hands up if you're going to Hamburg."
Passengers who were due on the cancelled flights have been told they can re-book free of charge, subject to availability, or some will be able to claim a refund.
A Stansted Airport spokesman said officials would work with the police to investigate how the breach occurred.
"If there are lessons to be learnt, that is what we need to take on board. We need to discover if there's anything we can do better.
"This is a site of about 2,000 acres bordered by a security fence. It is not operated as a fortress.
"The people were spotted very quickly this morning and the police and security staff were quickly on the scene.
"The first wave was intercepted before they got to the runway.
"The second wave was intercepted before they got through the fence."
He said passengers should check with airlines before leaving home as delays were likely to continue throughout the day.
"Ryanair decided to cancel their first wave of flights so, with luck, later waves should not be too badly affected.
"Other airlines decided not to cancel so they will have to try to catch up."
He praised the way the majority of passengers had responded: "I think most people have been in fairly good spirits even though their plans have been very badly disrupted."
The spokesman said BAA is happy to discuss airport expansion and respects people's right to protest within the law.
"However, any unlawful or irresponsible behaviour aimed at disrupting the smooth operation of the airport is unacceptable."
Essex Police said 50 of those arrested today were held on suspicion of aggravated trespass, three on suspicion of attempting to gain access to a restricted area and four of conspiracy to commit a public nuisance.
A force spokesman said a detective superintendent will head an inquiry into the incident but added that security at Stansted was primarily the responsibility of the airport authority.
Prime Minister Gordon Brown's spokesman told a regular daily media briefing in Westminster: "Of course everybody has a right to protest, but people also have a right to be able to travel without unnecessary hindrance."
A Greenpeace spokesman said: "The climate change secretary Ed Miliband called for a Suffragette-style movement to pressure governments to act. Well, he got his wish. The Suffragettes were disruptive and lambasted by the establishment of the day, but have been utterly vindicated by history, and no doubt it will be the same with Plane Stupid.
"The delays to passengers are unfortunate, but right now we're in the most important hundred months in human history as we try to beat climate change before it's too late - and the Government's plans to expand airports could destroy our chances before we start."
Sign company chief executive Terry Purton, 61, of Edenbridge, Kent, had been due to board a flight to Bratislava at 3.30am today.
"I just wish the protesters had left it for a couple of hours," he said.
"I do wonder about security. They did it to protest so it shows somebody more serious could as well. If they can do it, I'm sure there would be nothing to stop terrorists."
Mr Purton praised the way the situation had been handled by airport bosses.
"They've kept us informed," he said. "I just can't stand the queuing. They've come round and given us water. I don't think there's anything more they can do."
Student Andrew Montgomery, 25, from Glasgow had been set to fly home at 8.40am after visiting family in the London area.
Asked for his view on the protest, he said: "I think it's pretty bad. I don't think they should have been able to get where they did."
Teacher Anne Nordbye, 35, from Oslo, Norway, who spent the weekend Christmas shopping in London, had her 6.30am flight cancelled.
"The information has not been very good," she said. "Luckily, I have a brother who works at an airport in Norway so he has kept me up to date with what has been happening. Otherwise I would have been really in the dark and frustrated."
She added it was "worrying" that the protest had been able to take place.
"How did they do it?" she said. "That's what I would like to know. It's worrying. There must be cameras to spot this type of thing."
Nick Barton, commercial and development director of Stansted Airport, said the protesters arrived in an "old fire engine".
"At about 2.50am, we got notification that someone was trying to break in through security fencing," he said.
"Our airfield security turned up to intercept them. At the time, we believe they were using an old fire engine, which had been parked next to the fence.
"It probably didn't look out of place in all honesty as there are a number of emergency services vehicles around the site.
"They managed to cut through the fence. As soon as they were through, they ran through the gap they had created and brought the fence panels to barricade themselves in."
Mr Barton said it is thought protesters also arrived in other vehicles - and bicycles - as they converged on the airport.
"They must have come in other vehicles because clearly you can't get 50 people in a fire engine," he said.
"There were people on bikes but they were stopped by our security."
Mr Barton said there was never any possibility that the intruders could have reached the runway.
"Our site is 2,000 acres in size and the perimeter is enormous," he said. "But they were stopped well short of the runway.
"We are dealing with a security breach, which has caused the runway to be closed and flights cancelled, but at no time were any passengers or planes in danger."
He said he was confident all the protesters had been arrested.
And he criticised those behind the demonstration.
"It wasn't a peaceful protest - it was unlawful," he said. "There has been a lot of disruption, which Plane Stupid will no doubt be pleased about."
Robert Siddall, chief executive of the Airport Operators Association, said: "We're all for a really robust debate on this difficult area, but people travelling on business or trying to take a well earned holiday should not have to put up with this kind of treatment from career protesters.
"This kind of direct action won't stop climate change. Tough debate and action to reduce overall emissions is what will.
"That's why we would encourage Plane Stupid to join us in supporting the Europe-wide Emissions Trading Scheme, which we'll join in 2012 to achieve 20 per cent real cuts in CO2 by 2020.
"In the meantime they should campaign with us for £2 billion a year raised by the air passenger duty tax to be used to cut emissions, not just help plug the hole in public finances."
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