The program, which imposes stiff penalties on municipalities that have excessively high deforestation rates, effectively avoided 1.23 billion tons of carbon emissions during the period.
The new law has environmentalists not only concerned about its impact on the country but also that the measures will undermine progress at the up-coming UN Climate Summit in December, which Peru is hosting.
Since 2010, there have been 2,900 cases of illegal mining, logging and deforestation, however only 300 were judged.
Decision determines that Funai must finalize all demarcation process within two years. The process has dragged on since 2007.
Environment Minister in Peru requested the judiciary to take action against Adolfo Cayra for dismissing the judge responsible for overturning rulings that were favorable for illegal mining.