It was the 16th explosive device detected in four days.
No one has been hurt but hundreds of trains have been delayed and the spate of attacks has triggered fears of a surge in left-wing violence.
Federal police and prosecutors are now in charge of the investigation. Dozens of experts, some in protective clothing, are scouring railway tracks for clues. Police helicopters are hovering over railway lines to spot possible suspects.
"We are looking at a new dimension of left-wing violence which is extremely worrying," Interior Minister Hans-Peter Friedrich said.
"It is an attempt to comprehensively and systematically put at risk the working of a city which is of great importance," he told Focus magazine.
Over the summer, mystery attackers set on fire over 100 cars in mostly affluent districts of Berlin. Police have not discovered who was responsible but many politicians blamed left-wing radicals targeting the rich.
The latest attacks have reawakened memories of the deadly Red Army Faction attacks in the 1970s and 1980s which killed dozens of people, including some top establishment figures.
The series of arson attacks started on Monday. Most of the devices, which consist of bottles with flammable liquid, have not exploded although on Wednesday one caught fire.
Most bombs have been planted on tracks in the Berlin area -- one was on the high-speed link between Berlin and Hamburg.
Railway operator Deutsche Bahn has offered a reward of 100,000 euros for clues and federal prosecutors, who usually get involved only in cases of national security, say they suspect "anti-constitutional sabotage".
A group called the "Hekla Reception Committee -- Initiative for more Social Eruptions" claimed responsibility on Monday, saying it aimed to cause widespread disruption and it opposed Germany's part in the Afghanistan war.
Asked about fears of a new wave of RAF-type terrorism, Friedrich said historical comparisons were difficult.
"But we must be extremely vigilant and make sure that the readiness to commit violence seen in these attacks does not develop into a new form of left-wing terrorism."
Germany's intelligence service has for months warned about the danger of growing left-wing militancy. (Reuters)
