Indonesian logger and palm oil producer, the Korindo Group, is challenging some of the claims by environmental NGO, Mighty Earth.
The NGO has been tackling Korindo over its activities in Papua and Maluku for several years, forcing an investigation by the Forestry Stewardship Council.
Mighty Earth said Korindo used membership of the FSC to 'greenwash' its forest and habitat destruction.
But the company said it has been complying with Indonesia law, pointing out the FSC requirements are more stringent.
Mighty Earth wants the company dissociated from the FSC but the council, which is maintaining the company's membership, says Korindo has agreed to collaborate "to improve its environmental and social performance and to provide remedy for the possible impacts caused".
Mighty Earth said Korindo must return customary lands, resolve social conflicts and grievances, fairly compensate local communities for lost land, natural resources, and livelihoods, and restore damaged ecosystems.
It also said Korindo needs to finance the restoration of an area at least equivalent to that which it has destroyed over the past two decades.
Korindo said it has launched legal action against Mighty Earth.