Marubeni's Indonesian subsidiary, PT Musi Hutan Persada, large land concessions overlap with a number of the customary land tenures of local communities. These overlapping tenure and use rights, created when the PT-MHP concessions were granted, have been a source of significant social conflicts between the company and various local communities.

In January 2014, the Indonesian organization WBH and Rainforest Action Network filed a complaint against PT MHP's FSC certification. Communities located in the Martapura district were forcefully evicted from 2,700 hectares of land. Their crops and houses were destroyed in 2011. As of December 24, 2013 no conflict resolution process had been agreed to, between the company and the communities, to remedy their alienation from use of their lands, the destruction of their houses and crops and forced relocation. PT-MHP holds a FSC Controlled Wood certificate, with registration number SA-CW/FM-002179, issued by the Soil Association Woodmark, an accredited certification body with the Forest Stewardship Council (FSC).

WBH has also compiled evidence of cases in Muara Enim, OKU Timor and Musi Rawas districts of ongoing community disputes with PT-MHP over land tenure and use rights, including cases of forced displacement by armed security forces and the destruction of their homes, rubber trees and gardens.

Soil Association Woodmark broken their relationship with PT WBH, but in May 2014 PT MHP obtained a FSC certificate issued by SGS for 296,400.00 ha, with registration number SGS-CW/FM-010071.

In 2017 Marubeni was involved in new coal power projects (totaling 13 Gigawatt) in Botswana, South Africa, Egypt, Vietnam, Indonesia, Thailand, Myanmar, the Philippines and Mongolia. Many of these countries have no or little coal plant capacity, which means that they will be locked into a coal-dependent future for decades to come. Marubeni is the 11th largest coal power developer in the world by total planned coal power expansion capacity. Developing these plants will lead to heavily increasing the amount of CO2 into the earth's atmosphere and thereby accelarating climate change. Building new coal power plants is completely at odds with the Paris Agreement; every new coal power plant is inconsistent with limiting global warming to well below 2 degrees.

In 2013, a Marubeni subisdiary, PT Tanjungenim Lestari Pulp and Paper PT TEL, operating in the Indonesian province of South Sumatra, has claimed that the wood chips it uses as raw materials are sourced "from 100% plantation logs which are sustainable and FSC CW (Forest  Stewardship Council Controlled  Wood). However, in 2013 Greenomics published a report accusing PT TEL of sourcing wood from Sumatran Tiger Habitat, of not conducting a HCV forest assessment and of not being transparent about the wood chips it buys from 'community forests'.