"Following the end of the strikes at 2.30 pm, flight operations are stabilizing. But disruptions can be expected until the end of the day," the operator of Germany's biggest airport in Frankfurt, Fraport, said in a statement.
"We are still asking passengers to check the status of their flight before travelling to the airport and re-booking where necessary," the statement said.
Travellers were being advised to check in as early as possible as there could be queues, Fraport warned.
Union Verdi confirmed the action on Wednesday and by Thursday morning, Germany's biggest airline Lufthansa had cancelled around a third of their scheduled 1,800 flights for the day – both short and long-haul.
Airport ground and freight handling crew as well as security staff are all taking part in the strike.
“It's going better than expected,” said Verdi secretary Uwe Schramm, speaking from Frankfurt where almost no airport staff were working. Half of flights – around 550 – scheduled to leave or arrive at the country's biggest airport had been cancelled by 5am.
Strikes also affected airports in Munich, Düsseldorf, Hamburg, Hannover, Cologne/Bonn and Stuttgart.
In Munich, Lufthansa has cancelled 140 flights. Hamburg has cancelled 16 domestic journeys to Frankfurt and Munich. At Cologne/Bonn airport, 13 of the 80 afternoon departures and arrivals will not go ahead.
Staff at Berlin's two airports did not take part in the strikes, but around 33 flights to and from Tegel will not leaving – a knock-on effect from action in other hubs.
Verdi has been fighting for higher pay for airport staff for over a year, with regular strikes hitting Germany's travel hubs. As of yet, discussions have not been successful and the union's 3.5 percent pay rise request has been denied.
Strikes have brought public transport networks to a standstill for two days in row in regional states such as Berlin, Hamburg, Bavaria and Baden-Württemberg. Other services, such as kindergartens, have also been affected.
Despite Thursday's walkouts at airports, however, the situation appears to be calm and airlines insist that the impact so far has remained limited.
Air Berlin, Germany's second biggest airline, listed only a small number of six cancellations of flights from the major airports on its website.
Air France also said it would not be greatly affected with just a single flight to Cologne-Bonn airport cancelled so far.
And Italy's Alitalia said it did not expect any disruptions.
"It's all very calm. The airport and the airlines have mobilised additional staff to help passengers," a Fraport spokesman said.
The pay of more than 9,000 Fraport employees is aligned to public service sector agreements.
A spokesman for Munich airport, the country's second-biggest, said 130 flights had been cancelled so far, mostly by Lufthansa. In order to limit the anticipated chaos, airlines have been advising passengers to check online before travelling.
And Fraport has advised passengers booked on the cancelled flights not to bother turning up at all.
National rail operator, Deutsche Bahn, is mobilizing additional staff to cope with the expected increase in rail traffic as air passengers take the train instead.
Under an agreement between the rail operator and the airlines, passengers holding valid tickets for domestic flights on Lufthansa, Germanwings or Air Berlin can swap them for train tickets.
Verdi is planning further action on Friday, but a union spokeswoman said airports would not be affected.
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