They have complained at the slow pace of the rescue effort.
The BBC's Dan Collyns in Cusco says the rescue is now hitting its stride and the tourists should be out by the weekend, although the misery will continue for the thousands of Peruvians who have lost their homes and farmland to the floods.
More than 2,500 tourists have been rescued since Monday, officials said.
The evacuation has been done by age, with the elderly and children taken first.
American Karel Schultz, 46, told Associated Press news agency: "It's been an adventure, a bit more than we bargained for."
Some tourists had to rely on locals for food after cash machines dried up.
The government only seems to care about tourists, locals are suffering too
A number of hotels were reported to have increased prices considerably.
The train to the city of Cusco is the only means of transport on the last leg of the trip to the Machu Picchu ruins, and has been suspended since Saturday when it was blocked by one of 40 landslides in the area.
Five people are reported to have died, including two residents killed when their home was destroyed, and a trekker crushed while sleeping in a tent.
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