The strike was called by air traffic controllers, ground support staff and other airport personnel to demand better retirement benefits.
Government spokesman Marcelo Diaz said that “never in Chilean history” had there been such a large shutdown.
Several airlines operating in the South American country, including LATAM, Air France and Sky Airlines, had contacted affected clients to reschedule their departures free of charge.
But hundreds of passengers were nevertheless stranded at the international airport in Santiago, the country’s main hub.
“They told us to come three hours before our flight despite the strike, and now they tell us we’ll have to change,” said Nori Carrillo, whose flight to Colombia was cancelled.
“The problem is, people have hotel reservations at our destinations, and no one is taking responsibility for that.”
Civil aviation authority chief Maximiliano Larraechea urged travellers not to even try going to the airport.
“No flights will be taking off today,” he told journalists.
The strike affects all the country’s airports, which will only handle arriving flights and emergency air traffic, he said.
He estimated 70 per cent of the country’s 3,000 civil aviation workers had joined the strike.
The shutdown, which began at midnight, will affect a total of 70,000 passengers by the end of the day, the Santiago chamber of commerce said.
Labor minister Ximena Rincon condemned the strike as “illegal”, saying the workers were public employees.