* Union Verdi called on 5,000 employees to strike on Friday
* People queue for hours to get through security
* Passengers asked not to come to airport
* Fraport says no more security checks possible
* Lufthansa shares down 0.2 pct (Adds union apology, Fraport comment on expectations for Saturday, Lufthansa staff hands out vouchers)
By Victoria Bryan and Peter Maushagen
FRANKFURT, Feb 21 (Reuters) - A strike by security staff at Frankfurt airport caused dozens of flight cancellations and delayed thousands of passengers, bringing chaos to Europe's third largest hub on Friday, the busiest day of the week for travellers.
Trade union Verdi had called on around 5,000 staff who carry out security checks on passengers, baggage and freight at the airport to strike for the entire day to push for their pay to be brought into line with counterparts at other German airports.
Hoards of people jostling to get to the front of lines at check-in and service desks thronged the airport, which usually handles 150,000 passengers on a typical Friday.
Some 90 flights were cancelled, with Lufthansa scrapping nearly 40, but the biggest problem was getting people through check-in and thinly-staffed security, airport operator Fraport said.
"We're trying our best but it's a challenge," a spokesman said for Fraport said earlier. "We tried to inform people but the strike was called at such short notice."
The airport's terminals were still crowded on Friday evening, after Fraport halted security checks around 1330 GMT, advising passengers not to make the trip to the airport at all.
Several tens of thousands of people were affected by the strike, Fraport estimated.
Earlier in the day, passengers had booed striking staff as they walked through the terminal blowing whistles and waving placards saying: "We're worth it."
Union Verdi issued a statement apologising to passengers but said it had no choice but to call for a strike after wage talks failed to result in a deal.
"We get 11.70 euros ($16.04) an hour once our trial period is over. People in Stuttgart get 14 euros an hour but we're the ones working at Germany's largest airport and the work is getting more stressful," Nsimba Gore, a 32-year old security assistant, said.
Verdi said more than 90 percent of security staff due to work on Friday, at least 800 people, had joined the strike. The union's offer to let 110 people stand down from the strike for a short time to staff the security checks did not appear to ease the congestion.
The strike was called after four rounds of pay talks between Verdi and employers' association BDSW, which represents around 185,000 security staff who work for private companies, ended without agreement. The next round of talks is due on March 5.
David Irvine, a 56 year old project manager travelling from Scotland to Rome with his wife, had to queue for two hours to try and get his ticket changed.
"I've flown through here three or four times before, and it's usually pretty efficient, but today it's a disaster," he said.
Frustrated passengers tried in vain to get into security checks reserved for flight staff and ambulances lined up outside to offer medical assistance to people who had fainted after standing in queues.
"The air is thick, people are angry. I couldn't take it any more," Kristoffer Norberg, a 48 year old Swede travelling on business from Saudi Arabia, said. He decided to take the train to Stockholm instead.
Frankfurt DJ Shantel was trying to get to Istanbul but had been unable to get through security.
"I have no understanding for this," Shantel, real name Stefan Hantel, told Reuters, carrying a box of CDs. "I'm self-employed and have no union to represent me, but if I don't get to Istanbul today it means I lose a lot of business."
Lufthansa, itself often a target of strike action during pay disputes, sent staff from its headquarters next to the airport to help with distributing hotel vouchers and food.
Fraport said in the evening that it appeared nobody would have to camp out at the airport, adding air traffic was expected to start returning to normal on Saturday.
The BDSW is offering a two stage increase to 14 euros an hour, but Verdi wants hourly pay for its members to be increased to 16 euros with immediate effect.
"We just can't pay it," BDSW managing director Harald Olschok told reporters. "Our margins are between 3-5 pct, so if you want pay increases like this it will have to be passed on to customers and that will make it more expensive for everyone to fly."
$1 = 0.7293 euros Editing by David Holmes and Jane Merriman