Mohammed Adamu described rape as a serious and wicked offence and urged Nigerians to report any case.
Speaking to journalists after meeting President Muhammadu Buhari at the presidential palace in Abuja, the police chief said that 799 suspects had been arrested and 631 had appeared in court.
But Mr Adamu did not speak about the sentences or number of convictions. Activists are concerned that not many trials result in someone being found guilty.
Some of the recent victims were allegedly murdered after being raped prompting a series of protests across Nigeria demanding action from the authorities and communities.
The police chief said security agencies are partnering with non-governmental organisations in the areas of training, working with victims and evidence gathering for successful prosecutions as part of efforts to tackle the issue.