The government has banned copies of the report, titled Cambodia's Family Trees, although copies in Cambodian and English can be easily downloaded from the internet.
The report, which came out ahead of a June 19-20 meeting of international aid donors to pledge new assistance for Cambodia, also blamed donors for not pressuring the government over the alleged illegal logging.
In its first official comment on the report, the Cambodian government via its embassy in London released a statement saying the report's claims were "totally groundless, unacceptable rubbish".
Rejecting the charges it said that rather than losing forests, Cambodia was actively engaged in building up its forests.
"The policy of reforestation has been introduced and implemented while the ban on logging and deforestation has been well conducted and observed," the statement said.
The embassy added that Cambodia had terminated Global Witness's role as an official forestry monitor in the country in 2005 after it began a "political campaign" against the government.
Earlier this week Global Witness condemned the banning of its report as "senseless censorship" saying it would not hide the illegal destruction of Cambodia's forests.
"Attempts to suppress this report will not make the facts that it presents disappear," Simon Taylor, the group's director, said in a statement.
Taylor said the reaction to the report raises a serious question for Cambodia's international donors.
"Is the government sincere in its pledges to strengthen governance and the rule of law, or is it simply paying lip service to these ideals to secure aid and international respectability?'' he added.