Evidence is emerging of a wave of reprisal attacks and killings inside Gaza that have left dozens dead and more wounded in the wake of Israel's war.

Among the dead are Palestinians suspected of collaborating with the Israeli military. Others include criminals who were among the 600 prisoners to escape from Gaza City's main jail when it was bombed as the war began. Their attackers are thought to be their victims' relatives.

During and after the war, there have also been attacks on security officials from Fatah, the bitter rival of Hamas, the Islamist movement in control of the Gaza Strip. One witness told the Guardian how her brother, a Fatah military intelligence officer, was shot three times in the legs in an apparent punishment attack by gunmen from Hamas's armed wing.

The Israeli newspaper Ha'aretz reported yesterday that several Palestinian agents working in Gaza for the Israeli security services during the war had been killed, and cited one source as saying that agents were "intercepted" by Hamas because their intelligence had been used "carelessly" by the military.

Palestinians in human rights organisations are reluctant to speak publicly about what is a sensitive issue, but one respected human rights worker in Gaza said he believed between 40 and 50 people had been killed in reprisal attacks since the start of the war. But there was not yet enough evidence to suggest this was an organised campaign by Hamas, he said.

"We don't know who's doing the killing," the worker said. "Some are individuals, some might be from Hamas. It's been happening over several days, all across Gaza. It's not all necessarily Hamas actions against Fatah." Another human rights worker put the figure at between 25 and 30 documented cases of reprisal.

A human rights group in Ramallah, in the occupied West Bank, and funded by the Fatah-led Palestinian Authority, has protested. "A number of citizens have been extra-judicially killed during and after the Israeli military aggression on the Gaza Strip," the Independent Commission for Human Rights said in a statement.

"Fire was opened on affected citizens at a close distance. In addition, individuals in official uniform or masked persons opened fire on people's legs, severely beat others, imposed house arrests, and threatened to punish citizens along with their families if they would not comply."

Hamas dismissed the claims but said it had arrested suspected collaborators, apparently as part of an effort to reassert control over Gaza. "The internal security service was instructed to track collaborators and hit them hard," said Ehab al-Ghsain, a spokesman for the Hamas interior ministry in Gaza. "They arrested dozens of collaborators who attempted to strike the resistance by giving information to the occupation about the fighters."

One woman from near Zeitoun, south of Gaza City, described how masked men with ID cards showing they were members of the Izzedin al-Qassam Brigades, the Hamas armed wing, shot her brother in the legs. The family had fled the house but returned on 18 January, the first day of the Israeli ceasefire. At 8pm several gunmen appeared at the gate asking for her brother, a 36-year-old Fatah military intelligence officer who had not been working since Hamas seized control of Gaza in June 2007. The men searched the house for weapons, but found none and later left.

Early the next morning they returned. "They started firing in the air," said the 23-year-old sister, who declined to give her name for fear of further attacks.

"They asked him to put his hands up.They fired one shot into his left knee. He fell to the floor and started screaming and saying: 'I didn't do anything.'"

He was then shot in the right leg and again in the left. "They were holding us back and we were watching him bleeding," she said. The victim is now in a Cairo hospital after two operations on his legs.

She said several of his Fatah colleagues had been targeted: "It's a kind of revenge on Fatah. They thought they were responsible for what was going on in Gaza."

Separately, Hamas is believed to have stopped Palestinians reaching an Israeli field hospital on Israel's side of the border at Erez. "We don't care about it," said Hassan Khalaf, Hamas's deputy health minister. "They are just claiming they care about human beings but they don't."