The measure, announced yesterday in the official gazette, lasts for 60 days and comes more than a month after a spill was reported in Imaza district (population 23,000).
A second spill was reported on February 3 in Morona district (population 9,000).
Residents of both districts are overwhelmingly indigenous people.
The spills were on sections of the Northern Peruvian Oil Pipeline, which moves crude from the jungle over the Andes mountains to refineries through a lengthy route on the northern Peruvian coast.
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The state of emergency will provide humanitarian help for the communities and assistance in the cleanup.
In early February, President Ollanta Humala's government declared a health emergency in the region because the oil had polluted the rivers that provide drinking water to the affected districts.
The spill was due to pipeline deterioration, environmental investigators said.
As a result, PetroPeru was fined USD 3.6 million for failing to properly maintain the pipeline.
An indigenous rights group, the Interethnic Association for the Development of the Peruvian Rainforest, said last week that there have been 11 oil spills in the Amazon region since 2010.