Amnesty International, Human Rights Watch and Human Rights First had sought to send representatives to observe the trials, but the Pentagon responded that it planned to provide courtroom seating only for certain journalists and the International Committee of the Red Cross.
Amnesty International spokesman in Washington Alistair Hodgett has noted that the US State Department annually criticises other countries for closing trials to international monitors.
"It seems like that medicine can't be taken at home despite the US prescribing it abroad," Hodgett said on Tuesday, noting that his organisation has been permitted to observe trials in such nations as Libya and Egypt.
Hodgett said other countries that had refused to allow observers for trials include North Korea, China, Cuba and Myanmar.
While saying he was not suggesting US parity with those countries, Hodgett added, "There's a contrast here that ought to startle people who care about open-trial processes."
The three organisations strive to monitor sensitive trials around the world to assess them against international standards, including proceedings for war crimes and crimes against humanity.
"It seems like that medicine can't be taken at home despite the US prescribing it abroad."
The groups said they wanted to attend the US military tribunals to provide the world "independent and informed analysis of the trials."
Air Force Brigadier-General Thomas Hemingway of the Pentagon's Office of Military Commissions wrote in a letter to Human Rights Watch that "we will keep your request in mind" if the Defence Department was able to honor the request in the future.
Hemingway said no charges had been brought and no trials scheduled, adding the Pentagon had not formally named a location for the trials, although officials had made preparations for such proceedings at the remote base.
The organisations said the Pentagon was using space constraints at Guantanamo as a pretext to keep out rights activists who had been critical of the US plans to try some of the more than 600 non-US citizens held at the base under a set of trial rules specially devised by the Pentagon.
Critics say the rules are rigged to result in convictions.
The groups, which have been critical of the Pentagon's rules for the trials, protested their exclusion in a letter to Defence Secretary Donald Rumsfeld, saying "there can be no legitimate governmental reason for denying our access to the proceedings."