The report from Global Witness and the Environmental Investigation Agency shows that about 98 percent of the Madagascar wood -- mostly ebony, rosewood and pallisander -- is destined for the Chinese luxury furniture market.
"In China, Malagasy rosewood beds sell for a million dollars apiece, yet less than 1 percent of the profits remain with local people," EIA Executive Director Alexander von Bismarck said in a release. He noted that the group's investigations found that Chinese traders were often aware that the wood they purchased was endangered and not legally cut.
Madagascar's director general of forests, Julien Noel Rakotoarisoa told BBC News at the CBD meeting that the report broadly presented a "pretty accurate account" of the problem but said the situation was beginning to change.
Rakotoarisoa said his country issued the last export permit a year ago and no more permits would be issued.
He pointed to an unauthorized consignment of 300 tons of rosewood from Madagascar that was intercepted in the nearby Comoros Islands a few months ago as an example of action taken on illegal exports.
While Madagascar earlier this year reinstated a ban on the export of all precious woods, the report shows that further shipments of wood have left Madagascar's ports since then and logging continues.
An article in The New York Times also reported environmental groups saying the illicit trade has increased at least 25 fold in the last year, with the value of the timber totaling at least $167 million during that period.
The illegal trade has been facilitated by the weak law enforcement of the country's transitional government as well as complicity by some of the country's state authorities, the report states.
EIA and Global Witness called on China to take immediate action to halt imports of wood from Madagascar and adopt stricter policies for the country's traders and companies manufacturing products from the wood.
"China's response to these findings will be critical for Madagascar's biodiversity. China has a great opportunity to help put an end to illegal timber trade and protect biodiversity," said von Bismarck.
The lush rainforests of Madagascar, the world's fourth largest island, contains some 14,000 species of plants.
In July, the rainforests of the Atsinanana, the site of most of the illegal logging, were added to the List of World Heritage in danger.