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The incident occurred at the port of Iparia in the Amazonian region of Ucayali, according to a police report carried by state news agency Andina.
The exact number of people on board the vessels remains unclear.
The national emergency operations center (COEN) said one boat was carrying around 50 passengers, while the second had no passengers.
Navy captain Jonathan Novoa told AFP that nine bodies had been recovered so far, with 25 people injured and possibly around 40 missing.
Authorities are working with families at the site to determine how many people still need to be located.
Footage aired by UTV Noticias showed panicked residents running along the riverbank as bags, cargo, and personal belongings floated downstream.
COEN said the tragedy occurred at dawn due to erosion along the Ucayali River, and confirmed that the navy had been deployed to assist.
Novoa said fast-moving currents, whirlpools, and dense fog were complicating search operations.
“We are in the flood season… and at the time of the accident there was fog, making the tasks very difficult,” he added.