Half-term air passengers are being advised to arrive in time after passengers at Stansted and Birmingham airports had long waits on Monday.
Some people missed flights at Stansted on Monday
Some at Stansted missed their flights amid queues blamed on security checks, put in place after the alleged airliner terror plot in August.
A spokeswoman said many assumed checks had been relaxed, but "that is not so".
However, Gatwick, Heathrow, Manchester, Liverpool and Nottingham East Midlands said they had been operating as normal.
A total ban on hand luggage was initially brought in after the alleged plot was foiled on 10 August. Although the ban was eased in September, restrictions remain tight.
Passengers are still limited to one item of hand luggage, which can be the size of a small roller-suitcase (56cm x 45cm x 25cm, or 22in x 17.75in x 9.85in approx at many airports, and slightly smaller than this at Stansted).
No liquids are allowed through the security search point except some medicines, and baby milk and liquid baby food, which must be tasted by the passenger.
Musical instruments up to a certain size, pushchairs, walking aids and wheelchairs are also permitted in the cabin but will need to be screened.
Two hours before
"This is the first holiday week since those security measures were tightened," said the Stansted spokeswoman.
"And the increased numbers of passengers travelling this week has caused problems.
"Many have missed flights - I'm not sure exactly how many - although no flights have been cancelled.
"Our advice is that people should arrive at least two hours before their flight to give themselves enough time to check-in and get through security."
A Birmingham International Airport spokeswoman said: "We have had some delays with the increase in passengers during half-term but people are still bringing through liquids like perfume bottles.
"It's the first big test since the measures were introduced but also people's awareness is not as it was.
"People are not thinking about what they are packing before they fly."