Workers say they are unhappy over a planned merger between the airport authority and the national airline.
About 60 flights failed to leave Jomo Kenyatta International Airport - East Africa's largest - but some operations had resumed by the afternoon.
Airports in Mombasa, Eldoret and Kisumu are also disrupted.
The government has condemned the strike as illegal and Kenyan air force personnel have been brought in to ease the situation.
Riot police were deployed and used tear gas and batons to disperse striking workers at the capital's main airport, local media say.
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Kenya Airways says the situation is improving, with long-haul flights to Amsterdam and Mumbai having departed, others boarding and domestic flights "set to resume shortly".
Some flights to regional destinations have been cancelled.
A key figure in organising the strike, Kenya Aviation Workers Union secretary-general Moss Ndiema, has been arrested.
How are people reacting?
Frustrated passengers have complained of a lack of information and support from the authorities, with travellers waiting for hours with no update on their flights.
Some planes reportedly left without passengers.
Others voiced anger at the use of force to break up the protest.
The BBC's Lynne Wachira saw one man bleeding from the head, after being injured in clashes between workers and riot police.
What is the strike about?
It began at midnight local time (21:00 GMT on Tuesday). Fire engines were withdrawn from the runway, and security, check-in and baggage-handling staff also stopped working.
The unions are opposed to a plan that would see the loss-making Kenya Airways taking over the management of airports from the profit-making Kenya Airports Authority (KAA).
The aviation workers complain of unfair staff hiring, poor remuneration and that the proposed take-over would put their jobs at risk.
Image captionRiot police used batons and tear gas to disperse striking workers on Wednesday
Transport Minister James Macharia told journalists that jobs would not be lost in the merger, and branded the workers who caused the disruption "criminals".
"We have identified those who were involved and action will follow shortly," Mr Macharia said.
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