The San Diego County Sheriff's Department instituted the hotline after city staff and constituents alleged Filner had sexually harassed them, the Los Angeles Times reported Friday.
Filner said the hotline could produce an objective investigation rather than "press conferences and innuendo."
The San Diego Police Department reports to Filner, so the sheriff's office will be the lead agency should any investigation come from information provided through the hotline, officials said.
Three dozen people seeking signatures on a petition for a recall vote on Filner gathered outside City Hall as the announcement was made.
Three former supporters of the mayor demanded Filner, a Democrat, resign 10 days ago, accusing him of sexually harassing them.
Filner, 70, has refused to resign from the office he has held for seven months. He has apologized for behaving crassly toward women and promised to apologize to any women he may have offended.