Firemen found three women in the basement of a flooded house in the town of Simbach am Inn some 120 km (75 miles) east from Munich, police said.
In the nearby village of Julbach, emergency services found a drowned woman hanging over a tree trunk in a stream, police said, adding that her house had apparently collapsed.
At least two people were missing in the district of Rottal-Inn. "We're expecting the worst," police spokesman Michael Emmer said, adding divers were searching for those missing.
Police arrested two looters who tried to steal car radios. Several thousand households were cut off from electricity in the flooded region close to the Austrian border, an official said, Reuters reported.
Weather forecasters said more rain was expected in the region on Thursday, further complicating the rescue works.
Earlier this week, three people were killed in floods in the southwestern German state of Baden-Wuerttemberg and a young girl was killed by a train as she took shelter from the rain under a railway bridge.