The New York-based group said in a report that Iraq's National Security Services, which reports to Prime Minister Haider al-Abadi, runs a detention facility in Mosul. When granted access to that center on July 4, it was holding 427 men suspected of links to the Islamic State group, HRW said.
It added that the NSS first denied running detention centers, but later acknowledged it.
"National Security Service officials in Baghdad told us that the intelligence agency has no authority to hold prisoners but changed their line once we were able to see the prisoners for ourselves," said Lama Fakih, Middle East & North Africa Deputy Director at HRW.
"Baghdad needs to publicly clarify which authorities have the right to hold and interrogate detainees," Fakih added in the statement.
An NSS officer said those prisoners were previously held in a house before a new prison block was built following "pressure from Baghdad."
HRW said the cells at the Mosul facility are clean and air-conditioned, but extremely overcrowded.
The head of the NSS in Mosul told HRW that all the prisoners were wanted for IS affiliation and were interrogated before either being brought before an investigative judge or handed over to another security entity if that person was on one of their "wanted" databases.
All the arrests were made after obtaining a warrant, and all detainees had access to a judge and a lawyer within 24 hours of their arrest, he added.
At the height of its power, IS controlled nearly a third of the country after its 2014 offensive. In recent years, Iraqi forces backed by a U.S.-led coalition have gradually driven the militants from all the territory they once held. Iraq's government declared military victory over IS late last year.
In March, The Associated Press found that Iraq had detained or imprisoned at least 19,000 people accused of connections to IS or other terror-related offense. The AP's count was based partially on an analysis of a database provided by an official listing all 27,849 people imprisoned in Iraq as of late January.
Thousands more were believed to be held in detention by other bodies, including the Federal Police, military intelligence and Kurdish forces.
Copyright 2018 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.