Kazem Gharibabadi said the allegations have had highly negative ramifications and there must be a probe.
He however said evidence must be provided for such claims and then those who have violated the law must be dealt with seriously.
An unspecified number of protesters including both men and women were arrested during the recent unrest and deadly riots in Iran that erupted after the death of a woman in police custody in mid-September.
Some of the detainees have claimed they were mistreated by police and in jail.
