The deadly weather, which killed six people in western Germany on Monday night and Tuesday morning, moved east on Wednesday causing travel problems.
Rail operator Deutsche Bahn reported service interruptions on both the Hanover-Berlin and Hamburg-Berlin long-distance routes. As trains were being diverted, passengers have had to reckon with longer transit times.
In the west of the country, where storms devastated parts of North Rhine-Westphalia, rail schedules remained irregular at major rail hubs, including Essen and Düsseldorf.
Deutsche Bahn said numerous stretches of track in the state were still closed. Trains heading to the Ruhrgebiet were also stopping at Cologne, Hamm and Münster, while many S-Bahn services were cancelled on Wednesday.
Although thousands of Deutsche Bahn staff are trying to solve the problems, it is still uncertain when trains will be running on schedule.
Police plan to fly over each rail route in helicopters to determine the extent of the damage. Sixteen evacuated trains remained stranded on railways.