The letter says the protection of rights is essential ahead of elections scheduled for 2014.
"Your government continues to deny Fiji's citizens their rights to freedom of speech and expression, a free press, assembly, and association," the letter said.
"The military and police have arbitrarily arrested and detained human rights defenders, including trade union leaders and journalists, and others perceived to be critical of the government."
Commodore Bainimarama, who seized power in a 2006 coup and tore up Fiji's constitution three years later, has promised democratic elections in 2014, after a new constitution is in place.
The union groups also questioned the consultation process now underway before a Constitution Commission, saying the assembly that will review its proposals lacked political independence.
They say the Bainimarama government controls the assembly's composition and had given it the power to amend or delete recommendations from the commission.
"The interim government has unfortunately failed to protect key human rights essential if this consultation process is to be free, fully participatory, inclusive, and transparent."
The letter contained a list of grievances which the ITUC and Human Rights Watch held against the Fiji administration, including that it "consistently interfered in the workings of the courts" and "sought to limit public criticism through censorship of the press".
There was no immediate response by the government.
The Fiji Times has quoted Commodore Bainimarama as saying the Constituent Assembly to review the draft constitution "would consist of the broadest possible cross-section of Fijian society".