On Tuesday he stunned the court room when he took the stand and formally apologised for the deaths of more than 14,000 people at the S-21 torture and interrogation centre he ran in Phnom Penh.
No other former Khmer Rouge official has publicly accepted responsibility for the group's crimes. Pol Pot, the regime's supreme leader, died in a jungle hideout in 1998.
Aside from Duch, four other former Khmer Rouge leaders are currently in detention awaiting trial before the tribunal.
The group includes Nuon Chea, the Khmer Rouge's former deputy leader; Khieu Samphan, the former Khmer Rouge head of state; Ieng Sary, the former foreign minister; and his wife, Ieng Thirith, who was the regime's social affairs minister.
They have all denied any wrongdoing
But human rights groups have said many other former top Khmer Rouge officials remain alive and at large and should be brought to justice.
An estimated 1.7 million Cambodians died during the Khmer Rouge's rule over the country between 1975 and 1979.
|Hun Sen has said further trials may plunge Cambodia back into civil war [GALLO/GETTY]
But Hun Sen - himself a former Khmer Rouge commander - said the trials should not go beyond the other four charged with war crimes and crimes against humanity.
"If as many as 20 Khmer Rouge are indicted to stand trial and war returns to Cambodia, who will be responsible for that?," he said.
The joint UN-Cambodian tribunal did admit in January that an attempt to pursue more suspects was brushed aside by the Cambodian co-prosecutor, who argued it would not be good for national reconciliation.
Hun Sen's government has denied interfering with the tribunal, but rights groups suspect that the prime minister is keen to avoid an in-depth investigation for fear it will reveal secrets about senior Khmer Rouge figures inside his administration.
Hun Sen, 58, joined the Khmer Rouge during their 1970-75 war against the US-backed government of General Lon Nol.
He has said he defected to Vietnam in mid-1977 and played no part in the regime's slaughter of what amounted to about a third of Cambodia's then population.
Vietnamese troops invaded the country in late 1978 and installed a communist government made up mostly of former Khmer Rouge officials including Hun Sen, who became prime minister in 1985.