The airport said several flights were delayed by an average of 15 minutes as a result and three people missed their flights.
Security queues are normally less than ten minutes.
Members of the Unite union at Glasgow and Aberdeen Airports walked out at 4am in the first of a series of strikes by security and airfield staff, coach drivers and engineers.
The second is scheduled for 4am-4pm on Monday, with a third strike called at Glasgow Airport next Friday, 14 June from 4-8am.
The union today announced a fourth stoppage from 8:30am-2:30pm on Friday 21 June and threatened to escalate the action further.
Aberdeen Airport said there had been no disruption to flights or longer queues than normal.
The industrial action comes after a breakdown in talks about pensions and pay with airport owners AGS.
Unite accused the airport of withdrawing from negotiations over its proposal to close its pension scheme to existing members.
Passengers at Glasgow Airport took to social media to express frustration.
A Glasgow Airport spokesman said the security delays had been caused by other security staff taking over from those going on strike, with the queues longest around 6am.
He pledged there would be less disruption should the second strike went ahead on Monday, but said its morning peak was the busiest of the week.
He said: “We encountered longer than normal security times for a short period during our peak departure time and would apologise to our passengers for any inconvenience caused.
“It is important to highlight that the airport is fully operational and our contingencies are in place.
“We are working hard to ensure we keep any disruption to an absolute minimum during this period of industrial action and that our passengers remain our primary focus.
"We have learned from today and so are pretty confident for Monday."
The spokesman added that there had been no disruption to passengers being taken by bus to and from aircraft.
Pat McIlvogue, Unite regional industrial officer, said: “The industrial action has severely disrupted Glasgow Airport’s operations, despite the underhand tactics by management which included substituting fire safety officers with other staff on site who were questionably trained for the job.
"It’s a shame passengers’ travel has been disrupted, but this is 100 per cent the fault of Glasgow Airport management.“For the avoidance of doubt, Unite has repeatedly requested meetings with management and can categorically prove we wanted to meet any time this week to try and find a resolution to this dispute.
"But our overtures have been ignored, which is why we have added further dates for industrial action.
"If we continue to be ignored then we will have no option but to escalate this dispute.”
The airport said it had said all along it remained open to "meaningful dialogue" but the union's position had remain unchanged since the start of the dispute.
Steve Szalay, managing director of Aberdeen International Airport, said: “This is not a situation that we want to be in but it’s been business as usual here.
"We’ll have 10,000 people traveling today and they’ve been coming in and out without disruption."