The water level is causing havoc in a region where river vessels are used as the only form of transport.
The Amazon in the northeast city of Iquitos is 50cm lower than it was in 2005, according to officials in Loreto province.
It is the lowest reference point in four decades.
Low levels have brought economic havoc in areas of Peru that depend on the Amazon for shipping, by denying boats a navigable river as well as usable ports and harbours.
At least six boats became stranded for lack of river flow over the last three weeks.
Several shipping companies have been forced to suspend service, said regional civil defence chief Roberto Falcon.
River trips between Iquitos and other Amazon towns that normally take around 12-15 days now last twice as long, officials said.
The level drop, which is forecast to slide another 20cm until mid-September, has been caused by a lack of rain and high temperatures in the region, the national meteorological service said.
The Amazon is the second-longest river in the world, after the Nile, but discharges far more water at its mouth than any other.
It also drains more territory than any other, from Colombia, Bolivia, Ecuador, Peru, Paraguay and Venezuela before running across Brazil and into the Atlantic.
