There were no injuries in the pre-dawn attack on the U.S. company's headquarters in the Greek capital, located in the Maroussi suburb north of the city centre. There was no immediate claim of responsibility and authorities and the company said no warning call had been made before the attack.
While a motive was not clear, small armed anarchist or domestic terrorist groups have set off attacks in Greece for decades. They usually target official buildings, banks or symbols of state power with small bombs or incendiary devices and rarely cause injuries.
Police said initial information indicated three people had been inside the van. The hooded assailants forced the building's two security guards out at gunpoint before reversing the van into the front entrance, smashing the door.
They then triggered an incendiary device inside the van that police said appeared to have consisted of camping gas canisters and several containers of gasoline.
Police said accomplices were waiting to help them flee the scene in various directions, probably using motorbikes. The van used had been stolen from a nearby northern suburb about 40 days ago.
Microsoft spokeswoman Lia Komninou said the company had received no warning or threat before the attack or at any other time. The company, which has been in Greece for 20 years and employs 125 people, has been in that building since 2004.
Although they have died down over the past year, attacks had spiked following the fatal police shooting of a teenager in Athens in December 2008 that led to widespread riots across the country.
One group that appeared after the rioting had set itself apart by claiming responsibility for shooting dead an anti-terrorism police officer in Athens in 2009 and a journalist in 2010.