An independent investigation by the Harvard Law School has found that troops commanded by Myanmar's powerful interior minister and two other senior officials tortured and killed civilians over six years ago while fighting an ethnic rebellion.
Researchers spent four years collecting information about Home Affairs Minister Major General Ko Ko, Brigadier General Khin Zaw Oo and Brigadier General Mang Maung Aye, said the report released on Thursday.
They commanded troops during an offensive against rebels in eastern Karen state between 2005 and 2008, when soldiers fired mortars at villages and executed civilians, among other crimes, it said.
The report did not accuse the officers of directly ordering troops to commit abuses, but said they took place because of long-standing policies that sanctioned "the direct targeting of civilians and were designed to effect large-scale displacement."
"We've established that they had command and control over the forces that were committing these crimes," said Matthew Bugher, one of the authors of the report by the International Human Rights Clinic at Harvard Law School who handed over the report's findings to the government on Wednesday.
Information Minister Ye Htut, the only spokesman for the government, did not reply to phone calls and an e-mail from Reuters on the report. The military and defense ministry do not respond to reporters' queries.
Bugher said he had a "cordial but tense" meeting with Deputy Defense Minister Major General Kyaw Nyunt in the capital, Naypyitaw, to discuss his findings.
"The deputy minister of defense's response was that our report was one-sided and inaccurate," said Bugher, but he added that the fact the meeting took place at all was "remarkable and very encouraging".
"We do think it's problematic that there is a prolific human rights abuser in cabinet," said Bugher. "That casts doubt on the government's efforts to reform."
In March 2011, after 49 years of military rule, Myanmar's ruling generals ceded power to a semi-civilian government led by former general Thein Sein who initiated sweeping economic and political reforms. However, the military retains considerable control over the Southeast Asian nation.
The United States and others have voiced concern that reforms have stalled in some areas. On Wednesday, opposition leader Aung San Suu Kyi said political reforms had been stalled for months and accused the United States of being overly optimistic about the chance of progress.
The ruling party is composed largely of former military officers, and a military-drafted constitution reserves a quarter of parliament for unelected officers. It also stipulates that certain ministerial positions are reserved for the armed forces, including Home Affairs, which is held by Ko Ko.
The allegations come as U.S. President Barack Obama, a Harvard Law school alumni, prepares to visit Myanmar next week for a regional summit. A senior U.S. official told Reuters that Obama will not offer Myanmar any major rewards such as lifting sanctions or agreeing on military to military cooperation, because of concerns that the reform process has stalled.
A U.S. embassy official said on Thursday that the U.S. government takes the allegations in the Harvard report seriously and has for years raised its concerns about military abuses with the Myanmar government.
"We have repeatedly called on the government to provide justice for victims of these crimes and abuses and hold perpetrators to account in a credible and transparent manner," said the official.
Bugher aid the aim of the report was to spark a public conversation about military abuses during this period of Myanmar's much-touted reform and let the public discuss what to do about the military's legacy of abuse.
"We believe the transition and many of the reforms are remarkable, but there's an elephant in the room, which is the military and especially military conduct," said Bugher.
The military's image has been further tarnished over the past few weeks as news emerged that soldiers had killed a journalist they had detained in an area near the frontier with Thailand where there have been clashes between government forces and ethnic Karen rebels.
President Thein Sein last week responded to calls by rights groups and the United States government and ordered Myanmar's National Human Rights Commission to carry out an investigation into the incident and authorities on Wednesday exhumed the body of the journalist from a shallow grave in order to conduct an autopsy.