Small said the claims are "absolutely untrue."
"I never covered anything up in my entire career," he said.
Small said he couldn't comment on the allegations that the department didn't take disciplinary action, citing the confidential nature of personnel issues.
Roberts' attorney, John Barnett, was in trial Monday afternoon and could not be reached for comment, according to a woman who answered the phone at his law offices in Orange. He did not return a message left for him by an editor.
Roberts also faces 20 felony counts, including rape and forced sodomy against Mignosa, and rape and assault of his ex-wife.
The criminal case was investigated by the Orange County district attorney's office and the Orange County Sheriff's Department.
Roberts has pleaded not guilty to false imprisonment, making criminal threats, domestic battery, aggravated assault, dissuading a witness and vandalism.
The charges of rape, forcible sodomy and rape under duress were added in February.
The former officer's ex-wife filed a similar lawsuit against the city in November, asserting that city employees actively covered up alleged abuses against her while Roberts was employed with the Police Department.
Roberts was fired April 15 after being placed on administrative leave for several months. At the time, Small wouldn't discuss why Roberts was asked to leave the department.
If convicted, Roberts faces more than 23 years in prison.