The South Sudanese government made public a copy of the letter, dated May 3, earlier this month.
Aid workers say the South Sudanese military often behaves more as predator than protector. Its 200,000-strong force does nothing to stop tribal militias from razing villages and slaughtering civilians; but when it tries to disarm those militias, mayhem follows.
In a confidential letter sent to Western embassies in South Sudans capital, Juba, in the first week of May and obtained by McClatchy, an international aid organization accused the army of "severe and systematic" rights abuses in its campaign to disarm an ethnic minority, the Murle. The abuses included killings and widespread torture, beatings, rape and looting, the letter said. The agency, contacted by McClatchy, asked that its name not be divulged, saying it feared for the safety of its staff in the area.
South Sudanese forces in late April torched two Murle villages that constituted hundreds of homes, according to aid organizations that operate in the area, forcing hundreds of villagers to flee. Officials there confirm the general outlines of the reports.
"I dont know why they started to shoot the people," said Joshua Konyi, the county commissioner of Pibor, where the violence took place. "Theyd already collected the guns.
Such abuses are all the more awkward because the outside world is largely responsible for keeping South Sudan running.
Western donors have paid to staff the South Sudanese government with consultants from major international firms, including employees of KPMG, Deloitte, PKF and Crown Agents, who supplement government departments that often are staffed with former rebel fighters sitting at computer-less desks. In Juba, the foreign consultants are snidely referred to as "baby sitters" and they often have strict instructions not to interact with journalists.
Thats in addition to a massive United Nations peacekeeping mission mandated to support and mentor the government thats openly backed the governments abuse-ridden disarmament campaign. The U.S. has given nearly $300 million to the South Sudanese military and it embeds advisers to try to keep the army functional.
For up-close observers, the warning signs were there well in advance, like the horn of a freight train barreling down icy rails.
Gerard Prunier, a French scholar on Africa, is a harsh critic of the Sudanese government in Khartoum and was a strategic adviser to the South Sudanese government in the run-up to the January 2011 referendum in which South Sudanese overwhelmingly supported independence.
But he resigned before independence, and he explained his reasons in a phone interview with McClatchy earlier this month.
"What they are going to do is going to be so bad that I dont want to be guilty by association," he said. "The government in Juba is rotten to the core."
South Sudan denies that its incursion into Sudan in April was a long-planned military offensive. But diplomats and others report decisive evidence that the country regularly harbors, coordinates with and even fights side by side with rebel groups whose goal is toppling the Sudanese government.
In addition, South Sudans government released a new map in May that extended its claims to territory well north of its recognized border with Sudan. The map included areas that previously were considered undisputedly within Sudan.