Gross and illegal abuses against political opponents – including torture or ill treatment of arbitrarily held detainees – have been repeatedly committed by both Fatah and Hamas since last June, according to Amnesty International.

A detailed new report says the Hamas executive force in Gaza and the complex of Fatah-linked security forces in the West Bank loyal to the Palestinian President Mahmoud Abbas have each detained more than 1,000 supposed political opponents over the past four months in an "ongoing" struggle between the two factions.

Amnesty says the struggle is having "a dire effect on the lives of Palestinians, especially in the Gaza Strip, compounding and exacerbating the human rights and humanitarian crisis caused by Israeli military campaigns and blockades".

The abuses have occurred since the lethal faction fighting earlier this year in Gaza – also documented in the report – which preceded Hamas's takeover of Gaza by force in June, cost 350 lives in all and which Amnesty says showed "a flagrant disregard for the safety of the civilian population by launching indiscriminate attacks and reckless gun battles in residential neighbourhoods".

While acknowledging "a marked improvement" in internal security in Gaza in the weeks after the Hamas takeover, the report says that previous lawlessness was soon replaced with "internal repression" in Gaza with Hamas mounting targeted attacks on individual Fatah members or security force personnel, breaking up demonstrations and weddings at which Fatah slogans had allegedly been chanted, and attacks on and harassment of journalists trying to cover such events.

It says former detainees held by the executive force or Hamas's military wing said they were tortured, ill treated or "routinely" subjected to severe beatings. It says at least two detainees, Walid Abu Dalfa, 45, and Fadhel Dahmash, 31 died while in executive force custody during July.

Amnesty quotes the Palestinian Centre for Human Rights, whose representative was present during a post-mortem examination of Mr Abu Dalfa's body, as saying that it bore "bruises on the hands and legs, haematomas in the legs and signs of stranglehold".

The report quotes the leader of the executive force, Jamal Jarrah, acknowledging in August "some minor cases [of torture]" and pledging "to investigate all the violations and seriously address all the cases in prisons". Amnesty says, however, that there is no public evidence of measures to prevent further abuses.

The report also highlights "rife though much less well publicised" human rights abuses by West Bank security forces loyal to the emergency government set up in June by Mr Abbas. These include reports of torture and other ill treatment "becoming more frequent".

It says the emergency government – which enjoys the public backing of the international community and Israel – has failed to hold to account Fatah gunmen who have abducted, attacked or killed alleged Hamas supporters, or burnt down houses, businesses and charities suspected of links to Hamas – sometimes in full view of security forces.

It adds: "The arrest and detention of more than 1,000 presumed Hamas supporters, most of whom are not accused of any crime, stands in stark contrast to the Palestinian Authority's failure to arrest and bring to justice members of the [Fatah-linked] al-Aqsa Martyrs' Brigades."

The Palestinian Centre for Human Rights yester-day released the testimony of "MK" from Nablus who said he was tortured this month by personnel who said they were from the Preventative Security Service. The methods included forcing him to step up and down stairs 500 times and being hung on a wall.

Amnesty is calling for an independent commission to investigate the abuses.