The New York-based watchdog interviewed 42 children who were or have been detained, and made visits at several police stations and detention centers in Greece. Under international and Greek law, minors can be detained only in exceptional conditions. Human Rights Watch, however, found that many were detained arbitrarily and for longer than the maximum allowed period of 45 days.

“Children face extremely poor conditions. In some cases, they were made to live and sleep in overcrowded, filthy, bug- and vermin-infested cells, sometimes without mattresses, and were deprived of appropriate sanitation, hygiene and privacy,” according to Human Rights Watch.

The report also found that some minors were put in the same cells as adults, in breach of international and national law.

Because of shortages of space in dedicated centers, Greece detains children in protective custody while they await space in the shelter system, the report said. Greece has only 778 shelter spaces for unaccompanied children, but registered more than 3,300 unaccompanied minors just in the first seven months of this year.

A Greek government official said that there may have been cases of minors being detained longer than allowed, and that while conditions are far from perfect, the government is working to improve them.

“Changes are taking place month by month and they include efforts aimed at improving conditions and protection for unaccompanied minors,” the official said.

The report also found that minors in police custody often have little or no access to counseling, information, legal aid or schooling. Under international law, all unaccompanied children should be assigned a legal guardian, but none of the minors interviewed while in police custody had met their legal guardian, nor were they even aware they had one, the watchdog found.

The report echoes criticism expressed by the Council of Europe’s special representative on migration and refugees, Tomáš Boček, who in May called for urgent improvement of living conditions and protection of unaccompanied minors.

“The lack of any alternatives to detention seems to be one of the structural problems of the Greek system,” Mr. Boček wrote in a report at the time. The Council of Europe and its court, the European Court of Human Rights, are the main human-rights watchdogs on the continent.

In a case filed in March, five unaccompanied minors from Afghanistan sued Greece for the conditions and illegality of their detention, a spokesman for the court said.

—Stelios Bouras in Athens contributed to this article.