(Adds Cambodia tribunal system unlikely to be followed elsewhere, paragraphs 7-8)
By Prak Chan Thul
PHNOM PENH, March 11 (Reuters) - Under Cambodia's murderous Khmer Rouge, Meas Mut and Sou Met, now two-star generals in their 80s, are said to have hauled prisoners to S-21, a torture centre that symbolised the horrors of a regime that wiped out nearly a quarter of the population.
Another soldier, Im Chaem, now a Buddhist nun in her 60s, is suspected of running a forced labour camp where fellow Khmer Rouge cadres Ta An and Ta Tith oversaw massacres in the "Killing Fields" revolution of 1975-79.
Those allegations, contained in cases known as 003 and 004 at a UN-backed tribunal, are plunging Cambodia into soul searching over how far to pursue war-crimes accusations against former commanders, some of whom now occupy senior roles in government.
They are also fuelling criticism of the United Nations over whether its cash-strapped joint Cambodian tribunal will ever deliver justice for victims of the ultra-Maoist regime that tore Cambodia apart and was responsible for up to 2.2 million deaths.
The European Union, the second-biggest donor after Japan, has called on Cambodia to come up with more funding for the tribunal, where some workers went on strike last week after going for more than two months without pay. Cambodia says it has given more than its fair share and has appealed for bigger donations.
The tribunal's new American judge, Mark Harmon, said last month he wanted to reopen case 003 involving former Khmer Rouge navy chief Meas Mut and former air force chief Sou Met.
That puts him on a collision course with authoritarian Prime Minister Hun Sen, who has been accused of interfering to limit probes that could implicate powerful politicians. Meas Mut and Sou Met are now advisers to the Defence Ministry.
Internationally backed inquiries into years-old atrocities are almost bound to clash with present-day politics, such as the International Criminal Court's pre-election indictment of Kenya's new president for crimes against humanity.
Compounding difficulties in Cambodia is the fact that the court is a hybrid, as the Cambodians did not want to give up control, a formula unlikely to be followed elsewhere.
Hun Sen, a close ally of China which was a key supporter of the Khmer Rouge during the "Killing Fields" years, has vowed to prevent new indictments and has said he would be happy if the United Nations left Cambodia. He was himself a Khmer Rouge fighter before defecting to Vietnam, which invaded Cambodia and toppled Pol Pot's regime in 1979.
Almost every Cambodian alive lost a family member under the Khmer Rouge. Many fear the Extraordinary Chambers in the Court of Cambodia (ECCC), which began work in 2006 after an agreement between the Cambodian government and the United Nations to try those "most responsible" for the killings, will fail to bring justice.
The court, dogged from the outset by allegations of corruption, political interference and profligacy, had spent $175.3 million by the end of last year and handed down just one conviction - that of S-21's former prison chief, Kaing Guek Eav, alias "Duch", who was jailed for life for the deaths of more than 14,000 people. He has repeatedly said he was "just following orders".
Now on trial in the court's second case, known as 002, are the only remaining members of the inner circle of Khmer Rouge leader Pol Pot, who died in 1998: chief ideologue Nuon Chea, 86, former Foreign Minister Ieng Sary, 87, and head of state Khieu Samphan, 81. They may not live to hear the verdicts. Ieng Sary and Nuon Chea have been in and out of hospital for years.
Most of the suspects live in isolation away from the capital and have not talked about the accusations in public.
While Hun Sen's government has done little to stop case 002, it has reason to be concerned with 003 and 004: some government officials occupied Khmer Rouge positions similar to those held by the suspects.
CASE "REMAINS OPEN"
Harmon said case 003 "remains open and the investigation of the alleged crimes is proceeding" against members of Khmer Rouge navy and air force units for atrocities.
Harmon, who arrived late last year after two predecessors quit in quick succession, has urged victims of the crimes alleged in 003 or people with knowledge of them to come forward.
004, involving Im Chaem, Ta An and Ta Tith, was also under investigation by judges, the court said. Ta Tith is now a wealthy businessman.
The third and fourth cases have faced obstacles almost from the day they were initiated in 2008. Investigators and the public have struggled to gain access to case information, while financial difficulties threaten to shut the court down.
One former judge, Laurent Kasper-Ansermet of Switzerland, resigned a year ago after finding himself in "a highly hostile environment" with Cambodian judge You Bunleng, whom he accused of blocking investigations.
The cases would continue to divide the court, said Anne Heindel, an American lawyer and legal adviser to the Documentation Center of Cambodia, which researches Khmer Rouge atrocities.
"If (case 003) ever gets to trial chamber, it will be a new mess," she said.
Before Kasper-Ansermet resigned, he said four senior members of Hun Sen's ruling Cambodian People's Party (CPP) should be interviewed in connection with possible war crimes.
He identified National Assembly President Heng Samrin as a Khmer Rouge division commander when crimes were committed against Vietnamese civilians in 1977 and 1978, a court document showed.
The document also recommended interviewing Senate and CPP President Chea Sim, Senator Ouk Bunchhoeun and armed forces chief Pol Saroeun.
Kasper-Ansermet said investigators had discovered the Khmer Rouge attacked undefended villages and slaughtered whole families.
Prosecutors decided not to pursue these allegations, saying they had already been investigated as part of case 002 and were unrelated to 003.
"We are not interfering with the ECCC's work but facilitating them," said Cambodian government spokesman Ek Tha, who denied "any influence or authority whatsoever" over the court.
"Hun Sen decides everything in this country," said Henri Locard, a French historian of modern Cambodia who interviewed Im Chaem two years ago.
"I am protected by Hun Sen and I've done nothing," Locard quoted her as saying.
International donors, who already give Cambodia about $1 billion a year in aid, were reluctant to fund the controversial third and fourth cases, said Heindel, preferring the court to wind down with the second case as a successful legacy.
That case was suspended on March 4 when 20 court translators went on strike over unpaid wages.
Many Cambodians now accept that further Khmer Rouge prosecutions are unlikely.
"We want all people to stand trial but it's useless because it's up to this dictatorial government to decide," said Lorm Vichey, 57, who lost his mother and three brothers under the Khmer Rouge. "What can we do?" (Reporting by Prak Chan Thul; Editing by Jason Szep, Andrew R.C. Marshall and Nick Macfie)