The environmental group claims that the region is inhabited by endangered orangutan and mining activity could endanger them.
Mining activity in the region is likely to cause mass deforestation and damage the rivers of the upper Barito basin, it added.
The company has 75% stake in the project with the remaining stake is held by Indonesian partner Adaro Energy.
BHP Billiton reportedly planned to extract one million tons of coking coal from the region starting next year.
According to Friends of the Earth, the expansion of mining will extract of 770 million tonnes of coal.
Guardian Australia cited Friends of the Earth’s climate justice spokesman Nick McClean as saying: "These are sensitive forests full of biodiversity.
"There has been some logging of the lowland areas in the past but much of the area hasn’t been scientifically surveyed. We could lose species we don’t know anything about.
"We do know that river systems absolutely will be impacted. It’s alarming to think that BHP will be clearing an area simply to export coal that may not have a future."
