Clashes between the two sides peaked in June, when Hamas fighters forced Fatah-dominated Palestinian security forces from Gaza.
Mahmoud Abbas, the Palestinian president and leader of Fatah, dismissed the Hamas-led cabinet and formed his own government, which controls the West Bank.
Hamas, led by Ismail Haniya, the ousted prime minister, continues to govern Gaza.
In the report, the group said: "Arbitrary detentions and torture or other ill treatment of detainees by Hamas forces are now widespread and the initial improvements in the security situation which followed Hamas' takeover [of Gaza] are fast being eroded."
Speaking to Al Jazeera, Donatella Rovera, author of the report, said Hamas forces were now conducting a clampdown on Fatah supporters and anyone else critical of them in the Gaza Strip.
However, she said: "What we're finding in the West Bank is pretty much a mirror image, even though it is much less reported.
|"People find it surprising, what's happening in Gaza, buts its as if the international community doesn't want to see what's happening in the West Bank"|
Donatella Rovera, author of Amnesty International report
"People find it surprising, what's happening in Gaza. But it's as if the international community doesn't want to see what's happening in the West Bank."
The Abbas government condemned the report. A Hamas spokesman responded by saying his government wanted to "open a new page" through dialogue with Fatah.
In examples cited by the report, a child running to a shop to buy sweets was killed by shrapnel, a young woman going to a school exam died from a sniper bullet, and a peaceful march through Gaza City to demand an end to the clashes came under fire, and three civilians were killed.
In the Gaza Strip, members of Hamas' military wing act as police and have detained and tortured Fatah activists and critics. Hamas police routinely beat protesters to break up demonstrations, and have roughed up journalists covering the events, Amnesty said.
In the West Bank, security forces detained about 1,000 Hamas sympathisers and members, forcing many to sign statements condemning the group and disavowing their loyalties to it.
Although most were held briefly, many reported being ill-treated or tortured, the Amnesty report said.
The Palestinian Authority also ordered the closure of more than 100 charities linked to Hamas. Fatah loyalists have also acted against Hamas sympathisers with impunity, destroying Hamas-linked institutions, kidnapping and harassing loyalists.
Ashraf Ajrami, a minister in the West Bank government, said the report was baseless.
"I don't think they tried very hard to find out the truth," he said. "We have acted according to law."
Taher Nunu, a Hamas government spokesman, said his movement had acted out of necessity to put an end to chaos in Gaza.
"We regret the victims that fell during the internal clashes... Our concern was to defend civilians and our people," he said. "The solution to the disagreement is not by laying blame, but is by returning to dialogue and opening a new page."