In China, they discovered beds on sale for $1m, made from Madagascan wood.
The report was launched at the UN Convention on Biological Diversity (CBD) meeting in Nagoya, Japan.
Madagascan politics is split between factions associated with ex-President Marc Ravalomana and the rival who ousted him in a 2009 coup, Andry Rajoelina.
Conservation groups have previously warned that illegal extraction of timber and wildlife could flourish in this milieu, but the EIA/Global Witness is the first investigation to show the scale of the problem.
The two organisations were asked by Madagascar's national parks service to conduct the investigation.
This official endorsement enabled them to access records in government departments, such as cargo manifests and trade data.
But most of the details emerged through contact with the loggers and traders, who appeared - in written accounts and in video produced during the investigations - not at all concerned with keeping their activities under wraps.
Instead they were keen to take the investigators, posing as buyers, into the heart of the logging zone.
"Within one day we had the staff of the top boss in [the town of] Antalaha saying 'we'll take you into the National Park and show you where we cut wood for this German buyer'," Mr von Bismarck recounted.
The result was a four-day trek into Masoala National Park, part of a Unesco World Heritage Site - one where logging is seen to have been so serious that it was recently placed on the World Heritage In Danger list.
EIA and Global Witness also went undercover in China and other countries, discussing with people in the furniture trade where the wood came from and how much it was worth.
In China, its prime use is as reproduction furniture that can fetch extraordinary prices - such as the $1m bed.
An estimated 98% of the wood ended up in China, with the remainder going to the US and EU nations.
The recently-implemented Lacey Act, which makes an offence of importing illegally-logged timber, has reportedly deterred many buyers in the US. Last year it led to authorities mounting a raid on the world-famous Gibson guitar company over allegedly illegal Madagascan rosewood.
Broken promises
Speaking to BBC News at the CBD meeting here, Madagascar's director-general of forests, Julien Noel Rakotoarisoa, acknowledged the report broadly gave a "pretty accurate account" of the situation as it was.
But, he said, things were changing.
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End Quote Russ Mittermeier Conservation InternationalEven more serious is the illegal hunting of some of the country's most endangered and most charismatic flagship species that inevitably accompanies these logging activities”
He appealed to China to block the imports.
"If only they try to to work with the international community [on this]," he said.
"If they could... forbid importation, that would be a big step towards improving the situation."
This was a theme taken up by Alexander von Bismarck.
"In 2009, China issued a code of conduct for timber companies overseas," he said.
"If there is one example of a code of conduct being broken, it is clearly the companies that are stealing Madagascar's wood."
According to EIA's calculations, less than 1% of the wood's final value remains in Madgascar.
The Chinese delegation at the CBD meeting here did not respond to requests for comment.
Track record
Meanwhile, the Madagascan authorities are asking for the three woods to be placed on Appendix Three of the Convention on Interntional Trade in Endangered Species (CITES), which would require importing countries to obtain certificates tracking the wood from its point of origin.
Such certificates could not then be issued in Madagascar, as harvesting the trees is illegal.
But John Scanlon, CITES secretary-general, said the government had yet to submit the information required to secure listing.
"Madgascar has indicated an interest in putting these species on Appendix Three, but a number of things have to be done before they're eligible for listing," he told BBC News.
"We haven't yet got enough information to be able to proceed."
Mr Rakotoarisoa said he hoped the requisite documents would be with CITES early in the New Year.
Meanwhile, despite the withholding of export permits, illegal logging continues, according to Alexander von Bismarck.
"Less than two weeks ago, we had reports, with GPS co-ordinates, of logging within the National Park," he said.
Russ Mittermeier, president of Conservation International which runs a number of projects in Madagascar, said the country's political instability was having an impact on nature that went far beyond hardwood species.
"Perhaps even more serious is the illegal hunting of some of the country's most endangered and most charismatic flagship species that inevitably accompanies these logging activities," he said.
"For instance, the report provided evidence of lemur hunting in Masaola National Park, with the preferred target being the spectacular red ruffed lemur, a species found nowhere else in the world.
"The loss of this animal and many others threatened by such hunting would have serious consequences for Madagascar's ecotourism industry, one of its most important long-term sustainable sources of foreign exchange."