Out of more than 1,000 flights planned, 282 Friday had already been cancelled on Friday as airlines struggled to reassure their customers that they would get them to their destinations. Lufthansa and Air Berlin were offering passengers train vouchers for travel within Germany.
The strike involves 200 workers at Europe's third-busiest airport who are demanding better pay and working conditions. They are not trying to paralyze the airport completely, but rather force managers to the negotiating table.
“We will not back off,” said Markus Sieber, a board member with the GdF union that is organizing the strikes.
On Thursday, the airport's so-called "apron control" staff – who direct aircraft in and out of their parking positions – halted work at 3:00 pm until 10 pm.
It was decided to repeat the strike again from 8:00 am until 10:00 pm on Friday to increase the pressure on Fraport, the company that operates the airport.
The move was heavily criticised not only by Fraport, but also fellow trade union Verdi, which has accused the GdF of going rogue.
Fraport said it was training replacement employees and doing everything possible to keep flights landing and taking off.
"We've sufficient personnel to handle more than 50 percent – at the very least – of flight operations," Fraport board member Peter Schmitz told reporters on Thursday.
Fraport advised passengers to contact airlines directly, since it was primarily up to them to decide which flights would take off or land.
"We will ensure that flight safety is guaranteed," said spokesman Mike Schweitzer.
Travellers seemed resigned to having their travel plans disrupted with some voicing sympathy over the strike action.
Svein Marco Roszkowski, who had just flown in from Chile with his sister Jennifer and two children, said their onward flight to Oslo had been delayed for five hours.
"That's life. I guess people have a reason to strike," Jennifer said.
Jan Bucher of Germany, who was headed for Athens, said: "I have a two-hour delay. But I have an understanding for the strike."
The controllers' union has argued that apron controllers' pay does not take into account the additional complexity resulting from the opening late last year of a fourth runway in Frankfurt.
But Fraport denounced the action as "irresponsible" and "incomprehensible."
A board member of the powerful BDI industry federation, Dieter Schweer, said the strike would damage the whole economy.
"It is irresponsible and totally out of proportion," he said. "It is not acceptable that small groups in key functions paralyse critical infrastructures to push through their own individual interests."
National rail operator Deutsche Bahn said it would lay on extra trains and staff to cope with the large number of passengers expected to travel by train.