The controllers' union decided to join the nationwide pay protest late on Wednesday, catching many airlines by surprise.
The strike also closed public offices, schools and other services. Hospitals were reported to be operating with a skeleton staff. Public transport and banks were not affected.
Striking public sector workers, representing over 400,000 teachers and civil servants and health workers, are demanding above-inflation pay rises for 2003.
The flight cancellations left hundreds of passengers trapped at Athens airport and searching for an alternative way to reach their destinations.
"This is irresponsible, in such situation one has no way of warning the passengers," a spokesman for German flag carrier Lufthansa said.
Adding to the chaos, some 2,500 Athens airport workers were due to hold a three-hour stoppage on Thursday afternoon in solidarity with the public sector strike.
Public Works and Environment Minister Vasso Papandreou is reported to have been caught unprepared by the strike and was forced to take a helicopter to Thessaloniki.
Union officials said the controllers would handle emergency, military and VIP flights as usual, but until Thursday night, other traffic would be limited to one flight per destination for each airline.
Turnout for a union-organised rally through the streets of central Athens is reported to have been low.
The protesters are expected to march in front of the economy ministry and parliament later on Thursday.