Only about a third of traffic on major lines was running, the Deutsche Bahn said in a statement, adding that service would be assured on around 30 per cent of regional and city lines.
Launching its biggest strike since 2008, the GDL union called on its members to walk out yesterday on freight services and from today on long-distance and regional passenger services.
The stoppages -- on traditionally one of the busiest weekends because of a school holiday -- are due to last until Monday.
Deutsche Bahn slammed the new industrial action -- the fifth in recent weeks -- as excessive, accusing GDL chief Claus Weselsky of putting his own "delusions of omnipotence" and "thirst for power" before the interests of the train drivers and passengers.
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"With its 50-hour strike on a holiday weekend, GDL and its chairman Claus Weselsky has lost all sense of proportion," the company said in a statement.
"GDL is running amok," it added, pointing out the strike's impact on autumn school holidays.
"Strikes at such close intervals and on such scale are absolutely irresponsible and bordering on irrationality," the rail company's human resources director Ulrich Weber told Bild tabloid.
Deutsche Bahn said it had put on standby night trains with sleeping berths to help stranded travellers in Hamburg, Berlin, Frankfurt and Munich, although there had been little demand for them on Friday-Saturday night.
The magnitude of the industrial action was surprising in a country where warning strikes rarely last more than a day. The last time Deutsche Bahn was hit by an industrial dispute as serious as this was in 2007-2008.