The paper giant described the claims made in Greenpeace's report, entitled How Sinar Mas Is Pulping the Planet, as "inaccurate" and "misleading".
Greenpeace alleges that APP is destroying areas of rainforest in Sumatra, in particular, the Bukit Tigapuluh Forest Landscape – one of the last remaining rainforests areas of the endangered Sumatran tiger.
According to the charity, Indonesia has the fastest disappearing rainforest in all of the major forested nations in the world.
It said: "Despite repeated claims that APP is on 'a responsible path towards sustainability' and will soon have no need to pulp Indonesian forests to meet its fibre requirements, Pulping the Planet reveals… that APP continues to acquire and destroy rainforest and peatland to feed its pulp mills in Sumatra".
Greenpeace added that, rather than being upfront about rainforest issues, APP has "simply continued to make dodgy claims about sustainability".
However, Stuart Andrews, APP sustainability and stakeholder outreach manager, Europe, said: "For the record, we would like to state that the claims made against Indonesian policy and APP in this report are both inaccurate and deliberately misleading.
"We would also like to stress that as part of its commitment to transparency, APP opens its doors to credible and responsible NGOs and independent auditors to trace the Chain-of-Custody of its products, enabling them to better understand the sustainability aspects of its raw materials."
In a statement, APP said it was "absolutely committed to the sustainable development of Indonesia and is dedicated to supporting the Indonesian government and its policies of achieving its environmental and development objectives".
It added that all of APP's pulpwood suppliers' areas are subject to "rigorous multiple socio-environment assessments" and that its pulpwood suppliers develop 60% of their production forest concession area, while the remaining 40% is set aside for conservation.
Last year, APP denied allegations that it planned to carry out a large-scale logging operation in the natural forest area of the Bukit Tigapuluh National Park.
In the latest Greenpeace report, several companies were named as buyers of products from APP, including Paperlinx, the Australian paper merchant that is present in the UK through PaperCo, Howard Smith Paper Group and Robert Horne Group.
A spokeswoman for Paperlinx said its company operated "one of the industry's leading product stewardship systems".
She said: "We work in conjunction with internationally recognised certifications PEFC and FSC to ensure our procurement is robust and that no illegal fibres enter our supply chain.
"If there is any evidence of illegal fibre appearing in certified products, we would take immediate investigative action with both the certifier and the supplier concerned."