Indonesia lost 840,000 hectares of forest in 2012 compared to 460,000 hectares in Brazil, despite its forest being a quarter the size of the Amazon rainforest.
Indonesia has greatly under-reported how much primary rainforest it is cutting down, according to the government's former head of forestry data gathering.
UN and official government figures have maintained that the country with the third biggest stretch of tropical forest after the Amazon and Congo was losing 310,00 hectares of all its forest a year between 2000 and 2005, increasing to 690,000 hectares annually from 2006 to 2010.
Exact rates of Indonesian deforestation have varied with different figures quoted by researchers and government, but a new study, which claims to be the most comprehensive yet, suggests that nearly twice as much primary forest is being cut down as in Brazil, the historical global leader.
Belinda Arunarwati Margono, who was in charge of data gathering at Indonesia's Ministry of Forestry for seven years and is now on secondment at South Dakota university, calculates that nearly 1m extra hectares of primary forest may have been felled in the last 12 years than was recorded officially.
In the paper in the journal Nature Climate Change published on Sunday, Margano says primary forest losses totalled 6.02m hectates between 2000 and 2012, increasing by around 47,600 hectares a year over this time. Because previous estimates of forest loss have included the clearing of pulp plantations and oil palm estates the real loss of primary forest has until now been obscured.