There was "a serious deterioration of the human rights situation in Iran following Israeli airstrikes in June, succeeded by a domestic crackdown that has further constricted civic space, undermined due process, and eroded respect for the right to life," the mission said in a report.
Its release was timed with the publication of similar findings by the UN Special Rapporteur on human rights in Iran, Mai Sato.
The investigators faulted Israel for a June 23 attack on a notorious Iranian prison which authorities say killed "80 people, including prisoners, their family members, staff and at least one child," the report said.
"The Mission’s preliminary investigations indicate that the airstrikes struck civilian buildings in the prison complex," it added, "which do not constitute legitimate military objectives, and that the strikes on these buildings were likely intentional."
Iran's actions following the strike were also criticized, with the report alleging prisoners were transferred to other facilities were beaten and moved at gunpoint, adding that one female detainee reportedly died.
It urged an Iranian investigation on "any violations that may have occurred prior to, during and following the strikes." It said Iran had responded to the mission's request for information on the attacks but Israel had not.
21,000 people detained by authorities in the wake of the conflict include "lawyers, journalists, human rights defenders, and people who expressed their views on the conflict on social media," the mission said.
The rise in executions this year in Iran to the highest levels since 2015, it added, "appear to contravene international human rights law, thereby violating the right to life" for which judges could be held to account for crimes against humanity
It rapped Iran for what it called extraterritorial violation of rights by surveilling and intimidating dissidents abroad.
"These patterns appear to form part of a recurring system of repression," it said, "underpinned by systemic impunity."