An inquiry is to be held by senior police and Heathrow executives into how a man carrying a rucksack managed to breach security at the airport and run towards an aircraft on a runway.

Flights were disrupted as armed police and the fire brigade swarmed on to the northern runway just after 2pm yesterday when the suspect was spotted.

He dropped his bag and was challenged and arrested by officers before he reached the Tarmac. The northern runway was closed for a short time as armed officers pointed their Heckler and Koch guns at him. Some workers at the airport said that the man had jumped over a fence.

The incident came just 24 hours before the Queen was due to open the airport’s new Terminal 5. Buckingham Palace said that today’s visit would still take place. Explosives officers carried out a controlled explosion on the rucksack, which contained clothes.

A police source said that while they did not yet know the man’s motive they were confident that it was not related to terrorism.

One theory among workers at Heathrow was that he was a protester bent on causing disruption before today’s ceremony. Anti-aviation campaigners have announced that they are planning a peaceful protest at the terminal on March 27, the day that it opens to passengers.

More than 700 people have agreed to take part in a “flash mob” in the international arrivals area at 11am. They will remove their coats at the same time to reveal T-shirts saying “Stop airport expansion”.

BAA and the police are making special security arrangements to deal with any protesters who try to disrupt the operation of the terminal.

A BAA source said the difficulty was that the check-in and arrivals halls were open to the public. It would cause great inconvenience for people meeting passengers from their flights if BAA allowed only people with tickets to enter the terminal.

Gordon Brown said he was satisfied that everything was being done to ensure security at Heathrow.

The Prime Minister, speaking after arriving at an EU summit in Brussels, said: “I think the important thing about the Heathrow incident is that the person was detained, that all the security precautions went quickly into action, that he’s now being interviewed and that all possible steps were taken so that when this incident happened the arrest took place.”

A spokesman for BAA said: “Clearly this incident is a matter of some concern and will be fully investigated in conjunction with the police.”

Airlines cancelled 20 flights, which BAA said was a “reasonably normal figure”. Many flights were delayed for a couple of hours as the runway was closed and all aircraft were diverted to the southern runway.

It is the second time in recent weeks that security has been breached at the airport. Greenpeace protesters managed to board a Boeing 777 late last month before unfurling a banner opposing the airport’s expansion.

Scotland Yard confirmed that the man was seen at 14.05 on the northern runway of the airport. A spokesman said that they would be investigating how the man gained access to the runway. The airport is understood to have been testing security before the official opening of Terminal 5. The new building is a significant landmark in the airport’s expansion.

A BAA Heathrow spokesman said: “Airport police swiftly apprehended a man near the northern runway of Heathrow this afternoon. The police arrested the man at about 2pm within the airport perimeter. The use of the northern runway was temporarily suspended while police dealt with the incident. The incident ended at about 3.50pm when the northern runway came back into full use. The southern runway remained fully operational throughout. Some short delays have occurred as a result, but we expect to return to normal later this afternoon.”

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