Highlands and Islands Airports Limited (Hial) said the airports at Inverness, Dundee, Benbecula, Stornoway, Sumburgh in Shetland, and Kirkwall in Orkney were shut on Thursday.
The Prospect union said its members do not want to take industrial action but have been left with no choice after running out of patience with Hial in a dispute it says has been going on for more than a year.
In a statement issued earlier this week, Hial managing director Inglis Lyon said: "We sincerely regret this escalation of the pay dispute by Prospect members and apologise for the inconvenience that this has caused our customers.
"We continue to work closely with our airlines to mitigate the effects of strike action and I wish to thank them and all our staff who have worked extremely hard to implement contingency measures.
"Throughout this process, Hial has been fully committed to resolving this dispute.
"We are disappointed that our efforts to provide possible solutions have been rejected by Prospect and its claim has not altered and remains a wage increase of at least 10%."
Mr Lyon said the airport operator - a public corporation wholly owned by Scottish ministers - is bound by Scottish Government pay policy and cannot negotiate a separate settlement.
The airports closed to air traffic from midnight on Wednesday until midnight on Thursday.
David Avery, Prospect negotiations officer, said: "My message to those suffering disruption to their flights is clear - ministers and Hial have the power to end this strike today and to end this disruption but are choosing not to."
The Scottish Government said it encourages Prospect and Hial to return to discussions around a retention allowance for air traffic controllers and to work towards a resolution to the pay dispute.