Three armed men drove a stolen truck through the building's entrance, poured a flammable liquid on the floor and then set fire to it, Ekathimerini.com reported.
No injuries were reported and Greece's anti-terrorism squad has launched an investigation to find out who was responsible for the attack.
"Our priority is our people and we are grateful that there were no injuries and all the employees are safe," Microsoft said in a statement.
There was no immediate information on the extent of damage to the building.
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