The Afghan president, Hamid Karzai, has pardoned three men who had been found guilty of gang raping a woman in the northern province of Samangan.

The woman, Sara, and her family found out about the pardon only when they saw the rapists back in their village.

“Everyone was shocked,” said Sara’s husband, Dilawar, who like many Afghans uses only one name. “These were men who had been sentenced and found guilty by the Supreme Court, walking around freely.”

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Sara’s case highlights concerns about the close relationship between the Afghan president and men accused of war crimes and human rights abuses.

The men were freed discreetly but the rape itself was public and brutal. It took place in September 2005, in the run up to Afghanistan’s first democratic parliamentary elections.

The most powerful local commander, Mawlawi Islam, was running for office despite being accused of scores of murders committed while he had been a mujahedeen commander in the 1980s and a Taliban governor in the 1990s, and since the fall of the Taliban in 2001. Sara said one of his sub-commanders and body guards had been looking for young men to help in the election campaign.

“It was evening, around the time for the last prayer, when armed men came and took my son, Islamuddin, by force. I have eye-witness statements from nine people that he was there. From that night until now, my son has never been seen.”

Dilawar said his wife publicly harangued the commander twice about their missing son. After the second time, he said, they came for her. “The commander and three of his fighters came and took my wife out of our home and took her to their house about 200 metres away and, in front of these witnesses, raped her.”

Dilawar has a sheaf of legal papers, including a doctors’ report, which said she had a 17mm wound in her private parts cut with a bayonet. Sara was left to stumble home, bleeding and without her trousers.

When I met the couple in May 2006, they were in hiding and struggling to pursue the four men through the courts, petitioning the parliament, the president, human rights organisations and the United Nations. Sara and Dilawar say that one of the men involved in the attack used money and connections to repeatedly evade justice, particularly after his boss, Mawlawi Islam, became an MP and, they allege, was fully able to protect him.

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In January 2007, Mawlawi Islam was assassinated. However, the other three men accused of the gang rape were put on trial, found guilty and sentenced to 11 years in prison. Abdul Basir died in jail. The other two rapists, Nur Mohammad and Kheir Mohammad, were released last May. The commander was found not guilty.

A copy of the pardon was numbered, dated in May and appeared to bear the personal signature of Hamid Karzai. It recommended the men’s release because, it said, “they had been forced to confess to their crimes.”

When showed copies of the presidential pardon and court papers, President Karzai’s spokesman, Hamayun Hamidzada, was visibly shocked and said that if the documents proved genuine, Mr Karzai would be “upset and appalled.”

He said it was impossible that President Karzai could knowingly have signed a pardon for rapists, but refused to speculate on how the pardon could have come about. He promised an investigation into all aspects of the case, including the - as yet unsolved - mystery of Sara’s missing son.

He denied that there was one law for the rich and well-connected in Afghanistan and another for people like Sara. “There are difficulties - we’re rebuilding institutions, including our justice institutions and there are shortcomings, but the president and the government are committed to the rule of law on all equally.”

A UN human rights official said that, although she could not remember a similar case of the president giving a pardon in such a serious case, corruption in the police and courts was endemic.

The MP, Mir Ahmad Joyenda, said cases similar to Sara’s were actually becoming more common. The police and the courts, he said, were usually under the sway of local commanders. “The commanders, the war criminals, still have armed groups,” he said. “They’re in the government. Karzai, the Americans, the British sit down with them. They have impunity. They’ve become very courageous and can do whatever crimes they like.”

Sara and Dilawar are again in hiding, having felt too vulnerable to stay in their village. Dilawar was prepared to discuss the case. In Afghanistan, speaking about rape means risking further dishonour, but when asked whether he minded Sara’s story being publicised, Dilawar said, “We’ve already lost our son, our honour, we’ve sold our land to pay for legal costs and we’ve lost our home – what else can we lose?”