Airlines SAS and Norwegian, the two largest airlines using the airport, have had more than 500 passengers affected by the delays at security.
A total of 352 passengers who were meant to fly via SAS were rebooked to new departures due to long waiting times at security, according to SAS' head of communications Alexandra Lindgren Kaoukji.
"We understand the frustration and issues this situation is causing, and share our passengers' frustration," she told Danish newswire Ritzau in a written comment. "We know that Copenhagen Airport is working hard to solve the issue."
At Norwegian, Sara Neergaard, the head of the airline's Denmark branch, told public broadcaster that 200 passengers missed their flights on Thursday due to the long security queue, with another 30 missing their flights on Friday.
"Unfortunately we can't do much more other than asking people to come more than two hours before," she told DR. The airline has offered to rebook affected passengers onto new flights.
There were long queues on Thursday evening at Friday morning at Copenhagen Airport, due to new checks put in place by Denmark's Civil Aviation and Railway Authority, Trafikstyrelsen.
"The Civil Aviation and Railway Authority carries out constant checks of whether the airport is living up to security requirements in a long list of different areas," the authority said in a comment to Ritzau on Thursday evening. "As a result of our checks the authority has identified situations which mean that the airport needs to carry out some temporary additional checks at security."
It did not provide information on the reason behind the checks.
SAS is recommending that passengers arrive at the airport earlier than usual and leave extra time to pass security, with Lindgren Kaoukji adding that the situation at security had improved by midday on Friday.
The airport's head of communications, Lise Agerley Kürstein, told TV 2 on Friday that the airport does not yet know when the temporary checks will end, although she did say that they hope the issue will be solved early next week.
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