Thousands of people in the regions of Bavaria and Baden-Wuerttemberg had to leave their homes since torrential rain on Friday sparked deadly flooding.
More evacuations were called overnight into Monday as the huge volumes of water caused flood defences to fail.
In Bavaria, around 800 people were asked to leave their homes in the area of Ebenhausen-Werk after a dam burst early Monday.
Residents around Manching-Pichl, in the area worst affected by the floods, were told to shelter on the upper floors of their homes.
Speaking on a visit to Reichertshofen, in a flood-hit area north of Munich, Scholz said that such floods were no longer a "one-off".
"This is an indication that something is up here. We must not neglect the task of stopping man-made climate change," Scholz told journalists.
The floods were "a warning that we must take with us", he said.
- 'Never before' -
The Bavarian state premier, Markus Soeder, who accompanied Scholz on his visit, said there was no "full insurance" against climate change.
"Events are happening here that have never happened before," Soeder said, after a state of emergency was declared by districts across his region of Bavaria.
Around 20,000 people in Bavaria alone had been deployed to tackle the consequences of the flood, he said.
Police in Baden-Wuerttemberg on Monday said a man and a woman were found dead in the basement of their house in Schorndorf following the flood.
The same fate befell a 43-year-old woman in Schrobenhausen, Bavaria, whose body was found by rescuers earlier Monday.
The discoveries took the total killed by the floods to at least four, following the death of a volunteer fireman whose body was found on Sunday.
The 42-year-old volunteer died after his vessel turned over during a flood rescue operation.
Another volunteer, 22, was still missing after his boat also overturned overnight into Sunday.
A search operation to find the missing rescue worker had to be stopped due to the exceptionally high waters and strong currents, local police said.
The German Weather Service on Monday issued new warnings for heavy rain in parts of southern and eastern Germany.
- Rail delays -
The widespread flooding and continuous rainfall impacted transport in the region with widespread train cancellations and delays.
Train lines leading from Munich to Stuttgart, Nuremberg and Wuerzburg were unusable, rail operator Deutsche Bahn said.
A landslide near Schwaebisch Gmuend overnight into Sunday caused a high-speed train travelling between Stuttgart and Augsburg to derail, blocking the line. Nobody was hurt in the incident.
Despite Scholz's pledge to combat climate change, a panel of experts separately said Monday that the government's emissions forecasts through 2030 were unrealistic.
The government had underestimated future emissions in the transport, building and industry sectors, the climate panel said in a report.
Overall, the experts assumed that the government's emissions-reduction target for 2030 "will not be met".
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