The fee is "prohibitive ... in light of the spirit of larger goals" of the genocide trial, 23 Cambodian groups and the Bangkok-based Asian Forum for Human Rights and Development complained on Monday.
The association's request "practically and severely limits the freedom of choice of counsel afforded an individual, a legal principle that is recognised both by Cambodia and Cambodia with other nations," the statement said.
The issue became public last Friday after Cambodian and international judges finished a 10-day meeting to thrash out differences over the draft internal rules for the genocide trials, but said the legal fee dispute had prevented their adoption.
The international judges have also indicated that if the fee issue is not resolved, they may boycott a plenary meeting to finalise the rules.
Ageing Khmer leaders
Without the rules being formalised, the trials, which had been expected to begin this year, will face further delay, increasing the risk that elderly former Khmer Rouge leaders may never be brought to trial.
"The latest decision of the BAKC [Bar Association of the Kingdom of Cambodia] imposes a fee that is unacceptable to the international judges, who consider that it severely limits the rights of accused and victims to select counsel of their choice," the judges said in a statement on Friday.
The radical policies of the Khmer Rouge, who held power between 1975 and 1979, led to the deaths of about 1.7 million people through execution, overwork, disease and malnutrition.
None of the groups leaders have ever been brought to trial.
The tribunal was created by a 2003 agreement between Cambodia and the UN after years of difficult negotiations and arguments over the rules governing the trials have consumed nearly a third of the tribunal's three-year planned life span.
Pol Pot, the head of the communist government will not face trial as he died in 1998 but "Brother Number Two" Nuon Chea, Khieu Samphan, the former head of state and Ieng Sary, ex-foreign minister are all living in Cambodia and are due to face trial.
The only senior Khmer Rouge figure in detention is Duch, head of the notorious Tuol Sleng interrogation centre, a former school in Phnom Penh where at least 14,000 people were tortured and executed before a Vietnamese invasion ended their rule in 1979.