Merkel will travel to the hard-hit town of Schuld in Rhineland-Palatinate state, a spokeswoman for the regional interior ministry told AFP on Saturday, confirming earlier media reports.
The visit is set to take place in the afternoon, the spokeswoman said.
Merkel has called the flooding a national “tragedy” and promised support from the federal government to help the affected areas rebuild and recover.
German President Frank-Walter Steinmeier toured the town of Erftstadt in the western state of North-Rhine Westphalia on Saturday, to survey the damage from a massive landslide caused by the extreme weather.
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The main candidates in the race to succeed Merkel at September’s general election have all travelled to the stricken areas in recent days.
Merkel’s visit has been delayed because she only returned on Friday from a high-profile trip to Washington, her last official visit as chancellor.
Speaking alongside US President Joe Biden at the White House on Thursday, Merkel said her “heart goes out to all of those who in this catastrophe lost their loved ones”.