About 100 passengers were aboard the train, when the accident occurred at around 6:10 pm near the town of Riedlingen in Baden-WĂĽrttemberg state.
Contacted by AFP, police initially said four people had been killed before correcting their statement to three victims.
Authorities declined to elaborate on the number of injured or how seriously hurt they were, though tabloid Bild cited emergency workers saying there were 50 injured.
According to initial investigations by the police, the accident was probably caused by heavy rain, Welt reported on Monday morning.
"The water triggered a landslide in the embankment area towards the tracks, which in turn caused the derailment," the investigators told Welt.
German rail operator Deutsche Bahn confirmed several deaths and numerous injured. Two train carriages had derailed "for reasons yet unknown", it added.
Authorities were currently investigating the circumstances of the accident, the operator said, and traffic had been suspended over a 40-kilometre stretch of the route.
The passenger train was travelling from the German town of Sigmaringen to the city of Ulm when it derailed in a forested area.
According to the German Weather Service (DWD), thunderstorms moved over the region in the early evening hours.
In nearby regions, 30 to 40 litres per square meter fell in a short time, according to the DWD.Â
In a post on social media, German Chancellor Friedrich Merz expressed his condolences to the families of those killed.
He added that he was in close contact with both the interior and transport ministers, and had asked them to "provide the emergency services with all the support they need".
Footage from the scene of the accident showed yellow-and-grey-coloured train carriages lying on their sides, as firefighters and emergency services tried to get to the passengers.
According to local TV station SWR, helicopters arrived shortly after the accident to transport the injured to hospitals in the area, and emergency doctors from nearby hospitals were alerted.
Railway line closed
As of Monday morning, it's unclear how long the railway line will remain closed.
On the railway's website, the company wrote that rail traffic between Munderkingen and Herbertingen had been suspended. On Monday, according to the railway, replacement buses should transport passengers in the area.
Deutsche Bahn CEO Richard Lutz announced that he would travel to Riedlingen on Monday to get an idea of the situation and thank the emergency services personally.Â
German transport is regularly criticised by passengers for its outdated infrastructure, with travellers facing frequent train delays, and various technical problems.
The government has pledged to invest several hundred billion euros over the next few years, in particular to modernise infrastructure.
In June 2022, a train derailed near a Bavarian Alpine resort in southern Germany, killing four people and injuring dozens.
Germany's deadliest rail accident happened in 1998 when a high-speed train operated by state-owned Deutsche Bahn derailed in Eschede in Lower Saxony, killing 101 people.
With reporting by AFP and DPA.
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