About 250 climate change campaigners spent last night camping in tents in the building's car park - about half-a-mile from the protesters' main site in the village of Sipson.
The group was filmed by police cameras and monitored by up to 50 officers amid concerns the protesters were using the camp as a point from which to launch a raid on the airport's north runway just 150ft away.
A spokesman for BAA said today that staff had been told to stay away from Heathrow Point, the company's main administrative headquarters.
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Protesters camp outside BAA's HQ today
A woman is led away by officers today as hundreds of protesters descended on BBA's headquarters
He added: "The protesters have been there since about 3.00pm yesterday. We have told our staff not to come in to the building. Some of them are working from home, while others are working from other sites. This is not affecting our business."
One protester said: "We researched and planned this for a long while. We moved in stealthily yesterday and by the time the police were on to us it was too late. There will be further action. This site is better, though, as it is much closer to the runway."
The campaigners clashed with riot police yesterday as they laid siege to the offices as part of 24 hours of direct action which began at noon.
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Mounted officers chase a protester
Sleeping policewoman: a climate campaigner snaps a constable dozing in her patrol car at Heathrow today
A Scotland Yard spokesman said three protesters were arrested - for suspected drugs possession, intent to cause criminal damage and assaulting police. They are being held at West Drayton police station.
Before gathering at BAA, protesters marched out of the Camp for Climate Action and through Sipson waving banners bearing slogans such as "You Fly, They Dieî and "No Third Runway: Sipson Village RIP".
Skirmishes took place in a residential area near the BAA building as police armed with shields and batons blocked protesters.
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Police wrestle with a protester
A protester in full voice in the crowd of police and campaigners
Protesters attempt to break a police cordon in Sipson near Heathrow airport
Eight campaigners who blockaded British Airways' World Cargo Fresh Perishables Centre at Hatton Cross shortly after 9pm were arrested.
They halted vehicle access to the Eastern Perimeter Road depot by lying on the ground, locked together in a ring with arm tubes.
A camp spokesman said the protest was aimed at highlighting the growing level of greenhouse gases emitted by transporting food by air.
The activists argue that importing fruit and vegetables from developing countries encourages unsustainable farming practices and keeps farmers locked into a cycle of poverty.
The total arrests at Heathrow and Biggin Hill airports since protests began last Tuesday now stands at 58.
Protesters also targeted the Sizewell B power station, Suffolk police confirmed. Officers were dealing with eight campaigners who were attempting to storm the grounds. It was reported that the headquarters of BP in St James' Square was also attacked.
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