While likely to be welcomed by green groups, some do not think it goes far enough to protect remaining forests in the tropical archipelago.
The moratorium, which covers around 66 million hectares (254,827 square miles) of primary forest and peatland, was first introduced in 2011 and has been renewed regularly as part of the efforts to reduce emissions from fires caused by deforestation.
"The president signed an instruction on stopping new permits and improving primary forest and peatland governance," Forestry and Environment Minister Siti Nurbaya Bakar said in a statement.
Bakar said the Aug. 5 presidential instruction mandated that ministers, governors and other officials could not issue new permits within the moratorium area.
Indonesia has had one of the highest rates of deforestation in the world, with more than 74 million hectares (285,700 square miles) of rainforest - an area nearly twice the size of Japan - logged, burned or degraded in the last half century, according to Greenpeace.
The moratorium decision comes after authorities declared an emergency in six provinces on the islands of Sumatra and Borneo where smoke from outbreaks of forest fires have started causing acute respiratory infections.
The air pollution in Palangkaraya in Central Kalimantan on the island of Borneo was getting worse and had forced authorities to restrict school hours, said Arie Rompas, a Greenpeace Indonesia forest campaigner.
Rompas said the permanent moratorium still did not provide adequate protection for primary forest and peatland in the long run, blaming a lack of punishment and loopholes in regulations.
"The policy should not be via a presidential instruction because it is the weakest among legal instruments," he said.
According to the ministry's data, the area mapped out for the moratorium had been changed from 69.1 million hectares initially to 66.1 million hectares recently.
"If it's a permanent one, changing the map should not be allowed anymore," he said, adding that Greenpeace had found that permits for palm-oil, pulp wood, logging and mining had been granted on 1.6 million hectares from the original moratorium.