The report on detention says Israel's prison service held more than 9400 "security detainees" as of the end of June, and some have been held in secret without access to lawyers or respect for their legal rights.
A summary of the report, based on interviews with former detainees and other sources, decries a "staggering" number of detainees - including men, women, children, journalists and human rights defenders - and said such practices raise concerns about arbitrary detention.
"The testimonies gathered by my office and other entities indicate a range of appalling acts, such as waterboarding and the release of dogs on detainees, amongst other acts, in flagrant violation of international human rights law and international humanitarian law," UN human rights chief Volker Turk said in a statement.
Findings in the report, one of the most extensive of its kind, could be used by International Criminal Court prosecutors who are looking into crimes committed in connection with the October 7 attacks and its aftermath, including Israel's blistering military campaign that is ongoing in Gaza.
Authors of the report said its content was shared with the Israeli government.
The Associated Press has contacted the Israeli diplomatic mission for comment.
The war in Gaza erupted after Hamas ' surprise attack on southern Israel on October 7, killing some 1200 people that day and taking 250 others hostage.
Israel's retaliatory operation has obliterated entire neighbourhoods in Gaza and forced 80 per cent of the population to flee their homes.
Gaza's health ministry says more than 39,000 Palestinians have been killed, without distinguishing between civilians and combatants in its count.
