RANGOON, Burma — She thought for a brief moment that her husband had been beheaded as they dug his body from a shallow unmarked grave in eastern Burma. The reality was no less gruesome.

As a team of medics and police workers pulled the journalist from the ground Than Dar could see his head was in fact still there, but it was so badly crushed and deformed that it had looked—as the corpse lay embedded in wet mud—like there was no head at all.

“His skull was smashed, his cheekbones were broken, his jaw was dislocated and some of his teeth were missing,” Than Dar told The Daily Beast. “His body was buried very disrespectfully, they didn’t wrap him in anything and his underwear was showing.”

Par Gyi, 49, was killed early last month by the Burmese military, which in a rare move revealed the location of the body following nationwide protests and pressure from Britain and the United States for an investigation ahead of a visit this week by Barack Obama, who will arrive on Wednesday for the East Asia Summit.

The military says the freelance journalist, also known as Aung Kyaw Naing, tried to steal a gun and escape from custody four days after being arrested in late September. Army officials also allege that he worked for ethnic rebels as a “communications captain.”

Par Gyi’s wife, colleagues, rights groups and a large number of activists consider both claims to be brazen lies. And following the exhumation of his mutilated corpse last Wednesday they are more certain than ever that he died after being brutally tortured at the hands of Burma’s notorious army.

Than Dar said that medical examiners told her after the autopsy that they had found bullet holes in Par Gyi’s torso, face, one of his legs and one of his feet—five in total.

When she asked about the other injuries, the examiners said they would “talk about those in court,” she said.

The military’s story has “all the hallmarks of a cover-up,” said Shawn Crispin, Southeast Asia representative for the Committee to Protect Journalists.

“It’s more likely from the evidence available so far that Aung Kyaw Naing was tortured to death while in the military’s custody,” he added.

The killing is the latest in a series of flagrant attacks on Burma’s press that have convinced many that the country is backsliding on reforms just three years after it began emerging from half a century of isolation and military rule in 2011, when a nominally civilian government came to power.

President Thein Sein, a former general, has ended pre-publication censorship of the press, and he released hundreds of political prisoners, including nine journalists, in early 2012.

As a result, Burma was welcomed back to the international community. In a historic visit in 2012, Barack Obama hailed the “remarkable journey” the country had undertaken.

But the euphoria has long since faded. When Obama returns on Wednesday he will find a country where at least 10 journalists are behind bars, all convicted this year under draconian laws, and another is freshly buried.

International rights groups and local journalists have urged Obama to pressure Thein Sein to address these setbacks during his visit this week. Nay Phone Latt, a well-known blogger, said the U.S. president should call for the release of the country’s jailed journalists.

And in a letter published over the weekend the Committee to Protect Journalists urged Obama to “consider reinstating economic and financial sanctions” in response to the regime’s crackdown on the press, adding that he should “use U.S. influence” to ensure justice for Par Gyi’s killing.

“Last time Mr Obama was here … our government was improving,” Tin Oo, deputy leader of the opposition National League for Democracy party, told The Daily Beast during a Buddhist ceremony held for Par Gyi on Sunday. The reform process has “stalled,” he said, echoing recent comments by Nobel Peace Prize laureate Aung San Suu Kyi, the NLD’s leader.

Suu Kyi also said at a press conference last Wednesday that the U.S. “has been overly optimistic about the reform process.”

Par Gyi served on Suu Kyi’s team of bodyguards when she was a key leader in mass pro-democracy demonstrations in 1988. The family remain close to the democracy icon, who earlier this month sent a letter of condolences to Than Dar.

“He worked with us during the democracy movement ever since he was a student. All of us who endured hardship during that period share our condolences for Par Gyi,” she wrote. “I hope your family obtains justice.”

Despite the reforms, critical reporting on the powerful military has been met with severe punishments. That has included ten-year jail terms—later reduced to seven—with hard labor for five journalists who ran an expose on an alleged chemical weapons factory earlier this year.

Par Gyi went missing on September 30 after finishing an assignment reporting on fighting between the military and rebels from the Karen Democratic Benevolent Association in Mon state, southeast Burma.

On October 4 he was dead. The army kept his killing a secret and buried him in a hole just one and a half feet deep in the town of Kyaikmayaw, about 150 kilometers from the Thai border. Than Dar didn’t learn about his death until almost three weeks later.

After Par Gyi failed to show up for a family reunion with one of their three children in Chiang Mai, northern Thailand, she travelled to Mon state to find him. There she says she spoke to a military official who said he had witnessed Par Gyi’s arrest. She also met a police official who saw him in custody, and said he appeared to have been tortured, she added.

But neither could tell her where Par Gyi was being held, and it wasn’t until after she made a public appeal for his release that the army finally admitted he was dead, marking the latest setback for Burma’s hopes of achieving democracy.

Days before the exhumation, Thein Sein ordered an inquiry into the killing, but Robert Sann Aung, a lawyer representing Than Dar, told The Daily Beast the semi-autonomous human rights commission in charge of the inquiry is “biased.”

“The Human Rights Commission’s effort will be a non-starter unless the military gives its full cooperation,” Crispin added. “Unfortunately so far the military has acted to cover up rather than reveal the circumstances surrounding Aung Kyaw Naing’s shooting.”

When Than Dar arrived for the exhumation last week, she faced resistance from local government officials in Kyaikmayaw who didn’t want her to take the body back to Rangoon.

She said: “They said that because of a by-law I had to have the body cremated or buried within 24 hours after digging it up.” But Than Dar ignored them, intent on a traditional Buddhist funeral for her husband in Rangoon.

She got her wish, despite being stopped on the road from Mon state twice by monks and angry locals, who objected to the body passing through their town because of a traditional belief that it was bad luck. Police told her that if she chose to proceed with the body they wouldn’t be able to protect her.

The funeral went ahead Friday, attended by hundreds of friends and supporters. Some of Par Gyi’s old friends from Suu Kyi’s bodyguard team helped to inter the coffin in its tomb while others waved placards calling for justice.

On Sunday Than Dar held the last of the funeral rites for her husband with a food donation ceremony at a monastery. A life-sized poster of Par Gyi greeted guests at the entrance.

The Thar Du Kyaung monastery was a hotbed of political activity during a pro-democracy uprising in 2007 before being shut down by the military. On Sunday one of its halls teemed with activists, some of them former political prisoners, paying their respects.

“My children are traumatised,” Than Dar told a group of reporters in front a large reclining Buddha. “We should have rights as citizens and basic human rights.” Instead, once again, they are being stripped away.