The flooding, the heaviest in years, hit hardest in the Cuzco region in the Andes, the BBC reported Sunday.
Hundreds of villages in the regions of Puno, Ayacucho and Huancavelic also were damaged by torrential rain and were in need of emergency aid.
In Lucre, residents were trying to salvage belongings after a river over flowed its band and nearly washed away the town.
"Someone heard the noise and before we could even get out of our beds the water was flowing over them," Lucre resident Berta Pantoja told the BBC. "Terrified, all seven of us ran in different directions trying to escape."
The last of nearly 4,000 tourists was airlifted late late week after being stranded near the Inca ruins of Machu Picchu, where landslides washed out road and rail links to the site.
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