Filner resigned in late August after at least 17 women brought lurid sexual harassment allegations against the 71-year-old former 10-term congressman.
The felony count alleges false imprisonment "by violence, fraud, menace and deceit" but does not elaborate on the circumstances.
The victims were identified only as Jane Does.
San Diego County sheriff's investigators had been interviewing Filner's accusers and said they would deliver their findings to the attorney general's office for possible prosecution.
Filner attorney Jerry Coughlan did not respond to a request for comment.