Palestinian authorities have begun a rare military trial of security officers accused of torturing a Hamas suspect to death at a time of an intensifying crackdown in the West Bank against the Islamist movement.

Haitham Amr, 33, a nurse, was arrested by the Palestinian intelligence services, led by the Fatah political faction, at his home near Hebron, in the occupied West Bank in June. Four days later he was dead, his body showing extensive bruising and swelling, including near the kidneys. He had been suspected of membership of the armed wing of Hamas, the rival Palestinian faction.

He was the fourth prisoner to die in Palestinian custody in the West Bank this year. All were suspected of involvement with Hamas, none was ever charged and, apart from Amr's case, there have been no official investigations. In another high-profile case last year a Hamas preacher, Majd Barghouti, was also tortured to death.

Amr's death sheds new light on the often violent internal confrontation in the West Bank between the Fatah-dominated Palestinian security forces and their enemies Hamas, which won the last Palestinian elections and now rules over Gaza.

Many Hamas supporters have been arrested, and some have been killed. Last month Mahmoud Abbas, the Palestinian president and Fatah leader, sacked the mayor of Qalqilya, a Hamas supporter, and his 15-member council. While the Palestinian Authority says it is tackling terrorism, some Palestinians fear a slide into a police state.

Palestinian human rights groups say the abuse and torture of prisoners by Fatah-led security forces in the West Bank and by Hamas forces in Gaza is all too common. Three detainees have died in Hamas custody in Gaza this year.

The deaths come at a time when a $161m (about £100m) US-led effort is under way in the West Bank to train several battalions of the Palestinian National Security Forces, in preparation for possible future statehood.

At least 15 security officials have been investigated over the death of Amr, according to the Palestinian interior minister, Said Abu Ali. He said several officers were on trial at a military court, but he would not give their names or ranks.

Amr was arrested on 11 June. Three vehicles filled with security forces arrived at Amr's village, Beit ar-Rush al-Fauqa, in the southern hills of the West Bank. They told Abdullah Amr that his son was wanted for questioning but gave no explanation. "They told me they wanted Haitham for an investigation and that he would soon be returned," he said.

The official account of Haitham Amr's death was that he died after jumping from a second floor window of the Hebron prison while trying to escape. But the family and human rights workers say his corpse showed no sign of a fall but extensive and severe bruising, including near the kidneys, indicating he was beaten to death. The interior minister has since admitted Amr was tortured and died in custody.

Amr was, his father said, a Hamas sympathiser though not a militant. The rest of his family are strong Fatah loyalists, some of them even senior figures in the Palestinian security forces.

"My son was taken from my lap in order to be executed," said Abdullah Amr, 66, who has been a Fatah supporter all his life. "The authorities know everything. They know who killed my son and the Palestinian Authority is responsible for punishing them."

After Amr's death the authorities carried out a postmortem, but the report has never been released. However, Abdullah Amr, himself a nurse, examined his son's corpse before burying him and saw heavy, dark blue bruising and intense swelling on his legs and hips.

Investigators from al-Haq, a leading Palestinian human rights group, filmed the corpse and sent the video to a forensic pathologist in Geneva from the World Organisation Against Torture. The expert, Professor Patrice Mangin, wrote back saying he saw no signs of trauma that might suggest a jump from a second-storey window. He did see marks on Amr's wrists "consistent with tight and prolonged binding" and said it was "vital" to see the results of the autopsy.

According to Shawan Jabarin, head of al-Haq, torture in Palestinian jails is becoming widespread because of the growing divide and tension between Fatah and Hamas. Prisoners are often beaten, usually on the soles of their feet, or handcuffed in stress positions for hours – a notorious practice known as shabeh.

"They can stop the torture in one day by taking a clear position that anyone who commits crimes or torture will be brought before a court and punished," Jabarin said. "But all feel they are immune. This is the culture in security now. No one feels he is under threat."

Even though Palestinian law says a detainee must appear in court within 24 hours, suspects are being held without charge for up to six months, Jabarin said. Around 700-800 political prisoners are in West Bank jails, far more than in the past.

Abu Ali, the interior minister, admitted there had been a "violation of the rights" of Haitham Amr and an "excessive amount of force" in the interrogation. "Even if he was a Hamas member that doesn't justify the mistreatment that took place," he said.

Abu Ali, a former governor of Nablus and Ramallah who was appointed four months ago, admitted that abuse and torture had happened in other cases but said there had been a great improvement in law and order in the West Bank. In August he issued new directions about treatment of prisoners and said he was working to restore authority to the civil judiciary, away from the military, but that required, among other things, more prisons.

The Palestinian Authority in the West Bank was locked in a "war" with Hamas, he said. Security forces had found weapons and uniforms in raids on Hamas hideouts, a sign, he said, that the Islamist group wanted to create a security vacuum by undermining the Fatah-led security forces.

"They were preparing themselves to be an equivalent power to the Palestinian Authority," Abu Ali said. "In establishing a Palestinian state there is one authority, one law, one weapon … We will not allow what happened in Gaza to happen here under any circumstances."

* guardian.co.uk © Guardian News and Media Limited 2009