The Iraqi government has already announced an inquiry into the discovery of 173 malnourished, and in some cases badly beaten, men and teenagers, some of whom showed signs of having been tortured.
But given the high level of international concern and the importance of reassuring Iraqis, an internal investigation might not be enough, the UN High Commissioner for Human Rights said in a statement on Friday.
"In the light of the apparently systemic nature and magnitude of the problem, and the importance of public confidence in any inquiry, I urge the authorities to consider calling for an international inquiry," Arbour said.
"An international element would help the authorities address the problems in the system of detention in an impartial and objective way," she added.
Her call echoed that of Sunni Arab politicians who have demanded an international investigation into allegations that Shia militias linked to Iraq's Interior Ministry were behind the torture and abuse of prisoners.
The underground bunker, part of a fortified building near the ministry's Baghdad compound, was discovered by US troops during a search on 13 November in a development likely to fuel sectarian tensions ahead of 15 December parliamentary elections.
The detainees' discovery was a major embarrassment for the US-backed government, which has promised to deliver human rights after decades of dictatorship under former Iraqi leader Saddam Hussein.