Nearly two million people died during the regime
Former Khmer Rouge army chief Ta Mok, also known as "The Butcher", can only be held without trial until March next year.
The United Nations has been pressing Cambodia to bring Ta Mok and other former Khmer Rouge leaders to trial for atrocities carried out during their rule between 1975 and 1979.
But on Friday Hun Sen blamed the delays on the UN, repeating a threat to go it alone if the delays continued.
Legal delays
In August, Cambodia approved legislation for a tribunal presided over by three Cambodian judges and two foreign judges. But it has not yet got UN approval of the terms and conditions for the tribunal.
"The delay of the trial is not Cambodia's fault, it is the United Nations," Hun Sen told reporters on Friday.
"I want to ask the United Nations if it will participate or not. Please tell me clearly. Yes or no? If no, we will proceed on our own."
During the Khmer Rouge "killing fields" regime, 1.7 million people died through execution, torture, starvation and hard labour.
Under the agreement with the UN, the genocide tribunal will be held on Cambodian soil, but the UN is insisting that international standards of justice must be met.
Hun Sen will request parliament to extend the period allowed for the detention of Ta Mok and another jailed Khmer Rouge leader, Kang Kek Lue - the head of the S-21 torture and execution centre.
Kang Kek Lue can be held without trial until May.
The prime minister has repeatedly said he wanted the trial by the end of this year, but Cambodian government officials said on Friday that the UN had raised concerns about some aspects of the trial law and had requested changes.
Hun Sen said the UN was interfering with the country's legal system.
"I have no words to say," he said. "The UN wants an agreement with Cambodia which is above Cambodian law."
Critics of the tribunal say it will be a whitewash, because many of the most notorious Khmer Rouge leaders have already been given amnesty under a deal in the 1990s to end the country's long-running civil war.
Khmer Rouge leader Pol Pot died in 1998. Earlier this week the Cambodian tourist ministry announced plans to turn his jungle hideout into a museum reflecting the country's history.