Around 1300 people were missing in the Ahrweiler district south of Cologne, the district government said on Facebook. Mobile phone networks have collapsed in some of the flood-stricken regions, which means that family and friends were unable to track down their loved ones.
Some media have the death toll at more than 90.
Entire communities lay in ruins after swollen rivers swept through towns and villages in the states of North Rhine-Westphalia and Rhineland-Palatinate.
On Friday morning, houses collapsed in Erftstadt near Cologne, and rescue crews were struggling to help residents who had returned to their houses despite the warnings, the Cologne district government said on Facebook.
It said many people were still in the houses and several were missing. A gas leak was further hampering rescue workers as they tried to reach stranded people by boat.
One dam close to the Belgium border, the Rurtalsperre, was flooded overnight while another, the Steinbachtalsperre, was unstable.
The North Rhine-Westfalia parliament will hold an emergency meeting on Friday. German Interior Minister Horst Seehofer told magazine Spiegel that the federal government aimed to provide financial support for the affected regions as quickly as possible, adding it should go to the cabinet for approval on Wednesday.
In the town of Schuld, houses were reduced to piles of debris and broken beams. Roads were blocked by wreckage and fallen trees and fish flapped and gasped on puddles of water in the middle of the street.
"We have had two or three days of constant rain. Or maybe four, I lost track," said Klaus Radermacher, who has been living in Schuld for 60 years.
"I saw the pizza store getting flooded, half an hour later the bakery was flooded. There is a camping ground up there, so caravans and campervans came floating past, gas tanks. We were powerless against it. It came so fast, I've never seen anything like it."
Hundreds of soldiers and 2,500 relief workers were helping police with rescue efforts in Germany. Tanks were deployed to clear roads of landslides and fallen trees and helicopters winched those stranded on rooftops to safety.
The floods have caused Germany's worst mass loss of life in years. Flooding in 2002 killed 21 people in eastern Germany and more than 100 across the wider central European region.
Chancellor Angela Merkel expressed her dismay and vowed to help the affected communities rebuild.
"I tell those affected: we will not leave you alone in those difficult and scary times," she said during a news conference at the White House alongside U.S. President Joe Biden, who expressed his condolences to the victims. "We will also help with reconstruction."
In Washington for a farewell visit before she steps down following a federal election in September, Merkel said weather extremes were becoming more frequent which required action to counter global warming.
Pope Francis also extended his condolences to the victims and their families.
