A strike by security staff over pay paralysed two key regional airports in Germany for the second day in a row Friday, with more than half of flights scrapped.

At 10:30 am local time (0930 GMT), two thirds out of a planned 179 take-offs had been cancelled from Hamburg airport in the north of Germany, an airport spokeswoman said.

Just two security gates out of a total 20 were in operation, she said.

"The terminals are very full. Queues are very long," the spokeswoman added.

The day before some 117 departures and arrivals had been cancelled in Hamburg.

At Cologne/Bonn airport in the west of Germany, more than half of the 200 scheduled flights on Friday had been cancelled, according to the airport's website.

"Further cancellations are to be expected later in the day," it said.

The Verdi services union called the strike for security staff responsible for checking passengers and hand luggage, in a dispute with management over pay deals.

On Thursday, Duesseldorf airports had also been affected by the walkouts.