The cost of the weeklong strike could total 750 million euros (840 million dollars) and shrink gross domestic product in the second quarter 0.1 percentage points, Stefan Kipar at Munich-based Bayern LBbank said.
Joerg Zeuner, the chief economist at KfW, the government-owned development bank, said the strike, which began this week, presents "a definite risk."
"Considering the just-in-time production and the immense importance the rail has in delivering freight, the strike should cost us some growth in the second quarter," he said.
The drivers of freight trains began striking Monday afternoon, and the drivers of passenger trains walked off their jobs beginning at 2am (0000 GMT) Tuesday.
The strike is to last until 9 am Sunday, and there was no sign of a breakthrough in negotiations between the drivers union, GDL, and the rail company, Deutsche Bahn.
The long-running dispute centres on wages and labour rights. Train drivers have walked off the job eight times since September. Millions of commuters and travellers have been affected by the latest walkout.
Economists warned that the strikes could hurt Germany in the longer term as well. "A potential loss of reputation for Germany among foreign investors is a big risk," Kipar said.