Amnesty International says illegal detentions and torture have become commonplace in both Hamas-controlled Gaza and Fatah's West Bank stronghold.
It notes that the situation in Gaza has deteriorated sharply since June when Hamas seized control by force.
The UK-based group is calling for an independent investigation.
According to Amnesty, arbitrary detentions and the torture of opposition supporters have become widespread in the Gaza Strip where there have also been attacks on demonstrators and journalists covering such incidents.
But the report says human rights abuses are being committed in the West Bank too, by government security forces under the control of President Mahmoud Abbas against Hamas supporters.
Hundreds of Hamas sympathisers have been arrested and reports of ill-treatment and torture are frequent but much less publicised than Hamas violations, Amnesty notes.
"The leaders of both the PA [Palestinian Authority] and Hamas must take immediate steps to break the cycle of impunity that continues to fuel abuses, including arbitrary detentions, abductions, torture and ill-treatment by their forces," said Malcolm Smart, Amnesty's Middle East programme director.
"The ongoing factional struggle between Fatah and Hamas 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," he added.
Tensions between the two main parties have been high since the beginning of last year when Hamas defeated Fatah in parliamentary elections.
Those tensions often spilled over into violence and have led to the deaths of hundreds of people.
The distance between the sides has grown such that there is now little political dialogue between them, the BBC's Aleem Maqbool reports from Ramallah in the West Bank.
Amnesty's report calls on the international community to cease the sale of weapons to both factions until guarantees can be secured that they will not be used to violate human rights.
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