Coffee industry giants Nestle and Kraft Foods were both implicated in the report, published by the World Wildlife Fund, which says growers in Indonesia had illegally used 45,000 hectares of the country's Bukit Barisan Selatan (BBS) National Park.
The news threatens to be another public relations nightmare for top coffee firms amid ongoing criticism of their supply chain practices. The BBS park is an important refuge for endangered tigers, rhinos and elephants.
WWF said most of the coffee firms involved were unaware of the problem due to a lack of planting regulations in the region.
But it criticised both importers and exporters for not having mechanisms in place to prevent the trade of illegal beans. The group estimated from satellite images, interviews and tracking that 19,600 tonnes of beans were produced illegally every year.
"If this trend of illegally clearing park land for coffee isn't halted, the rhinos and tigers will be locally extinct in less than a decade," said Heather Sohl, of WWF UK.
Colleague Nazir Foead, of WWF Indonesia, said: "WWF doesn't want to shut down the coffee industry in Lampung Province.
"But we're asking multinational coffee companies to implement rigorous chain-of-custody controls to ensure that they are no longer buying illegally grown coffee, and we're asking the Indonesian Government to better protect the park."
Nestle sought to distance itself from the illegal beans on Friday. "We share the concerns of the WWF and we are in talks with them. It is an industry-wide issue," a spokesperson told BeverageDaily.com.
"It's true that sometimes determining its source can be problematic, but we would never [knowingly] buy illegally grown coffee." The group sources less than five per cent of its coffee from Indonesia and 60 per cent of that comes direct from farmers.
Kraft Foods was unavailable for comment.
Indonesia is the world's second largest exporter of Robusta coffee beans, many of which are grown next door to the BBS park, in Sumatra.
The WWF report will be a blow to the coffee industry as it attempts to show fairer treatment for producers in developing countries.
Coffeehouse chain Starbucks, which was not implicated by the WWF report, this week announced it had increased average prices paid for its coffee from $1.28 to $1.42 per pound between 2005 and 2006.
The group has become entangled in a fierce war of words with campaigners recently over its practices in Ethiopa, which depends largely on coffee for export revenue.