The federal police are investigating the incident, Interior Minister Nancy Faeser said, adding the motive for it was unclear.
The disruption raised alarm bells after NATO and the European Union last month stressed the need to protect critical infrastructure after what they called acts of sabotage on the Nord Stream gas pipelines.
"It is clear that this was a targeted and malicious action," Transport Minister Volker Wissing told a news conference.
A security source said there were a variety of possible causes, ranging from cable theft - which is frequent - to a targeted attack.
Omid Nouripour, leader of the Greens party, which is part of Chancellor Olaf Scholz's federal coalition, said anyone who attacked the country's critical infrastructure would receive a "decisive response".
"We will not be intimidated," he wrote on Twitter.
"Due to sabotage on cables that are indispensable for rail traffic, Deutsche Bahn had to stop rail traffic in the north this morning for nearly three hours," the state rail operator said in a statement.
Deutsche Bahn (DB) had earlier blamed the network disruption on a technical problem with radio communications.Â
Spiegel magazine said the communications system was down at 6.40am.
At 11.06am, DB tweeted that traffic had been restored but warned of continued train cancellations and delays.
The disruption affected rail services through the states of Lower Saxony and Schlewsig-Holstein as well as the city states of Bremen and Hamburg, with a knock-on effect to international rail journeys to Denmark and the Netherlands.
They came the day before a state election in Lower Saxony where Scholz's Social Democrats are on track to retain power and the Greens are seen doubling their share of the vote, according to polls.
Queues rapidly built up at mainline stations including Berlin and Hanover as departure boards showed many services being delayed or cancelled.
