There are also fears that more industrial action could take place in the run up to Christmas, which is one of the busiest times of the year, if the dispute is not solved.
Although services have been returning to normal after the so-called 'warning strike' by railway workers early Monday morning, there are still some logistical problems, according to train operator Deutsche Bahn (DB).
Some train delays and cancellations in the long-distance services are likely to take place on Tuesday, DB said, because vehicles and staff are not where they should be according to the timetable, following the industrial action.
Passengers have been urged to check if and when their train is running, before they set off on their journey. According to the DB spokesman, regional and suburban rail traffic, including S-Bahn services, should run according to the timetable.
The strike, which was held over a pay dispute, affected millions of passengers, with many left stranded or forced to take alternative transport.
SEE ALSO: Rail strike causes chaos throughout Germany
High speed ICE trains were cancelled throughout the country due to the four-hour strike which began at 5am. Regional services plus the S-Bahn network were also hit.
Meanwhile, the strike also had an impact on other forms of public transport such as U-Bahn services and buses as passengers piled on to them in a bid to get to their destination.
Some 1,400 trains, including cargo services, were affected, DB said.
DB customer service offices were also affected, meaning that in many stations passengers were left without information over loudspeakers or display boards.
The industrial action came after talks broke down Saturday between the DB and the EVG rail workers' union, which is demanding a 7.5 percent salary rise for 160,000 employees.
DB said that purchased tickets would remain valid up until and including next Sunday (December 16th) or could be refunded.
Passengers in Hamburg during the strike. Photo: DPA
Negotiations continue on Tuesday
The trade union and DB were getting ready to return to the negotiating table on Tuesday.
"With the warning strike, our colleagues have impressively demonstrated how serious they are about their demands," said Regina Rusch-Ziemba, the EVG's negotiator. "This strengthens us in our negotiations."
Both sides will meet in Berlin around 2pm.
Rusch-Ziemba added: "Our ultimate goal is to achieve a result at the negotiating table."
Pay negotiations ended without agreement on Saturday, and resulted in the industrial action.
Members of the union demonstrated at stations across the country during the strike, holding placards calling for fairer wages.
DB had described the strike as a "completely unnecessary escalation", insisting its offer was "attractive and met the main demands" of employees.
DB had offered a pay rise of 5.1 percent in two phases, with an option for staff to take extra time off instead, and a one-off payment of €500, DPA reported.
The rail operator is also in talks with a separate smaller rail union, the Union of German Locomotive Drivers (GDL). They have warned that their 36,000 members could also take action over a wage dispute if talks fail.
DB and GDL are also expected to resume negotiations on Tuesday in the city of Eisenach. GDL wants a 7.5 percent salary increase for its members too.
For more information on affected trains in your area visit the DB updates page.