Kilpatrick and Ayanna Kilpatrick were together at their mother's house Saturday, a day after he was released from jail for violating bond in a separate perjury case, said Doug Baker of the Michigan attorney general's office.
The mayor is charged with assaulting two investigators who were trying to deliver a subpoena at his sister's house in July in the perjury case.
In a court filing, Baker said the mayor had been ordered to have no contact with witnesses.
Kilpatrick's defense team, however, believes the mayor is not in any trouble. Attorney Jim Thomas said Magistrate Renee McDuffee clarified Friday that Kilpatrick could have contact with his sister.
In a statement, Kilpatrick spokesman Marcus Reese accused state Attorney General Mike Cox, a Republican, of trying to score political points with the latest filing against the embattled Democratic mayor.
36th District Court Judge Ronald Giles will hold a hearing on the matter on Tuesday.
Giles is the judge who sent Kilpatrick to jail Thursday for violating his bond conditions in a perjury case involving Kilpatrick and a former top aide. The mayor traveled to Windsor, Ontario, for city business July 23 without first notifying authorities.
Baker's filing asked the court to look at what happened and amend the terms of Kilpatrick's bond. The document doesn't mention any possible changes, and Baker left court without speaking to reporters.
Kilpatrick was released Friday after a higher court, acting on an appeal, set his bond at $50,000.
Baker referred to the perjury case by saying the mayor has "demonstrated an inability to adhere to reasonable bond conditions."
Kilpatrick and his former chief of staff, Christine Beatty, were charged in March with perjury, obstruction of justice and misconduct in office. They will be arraigned Thursday in Wayne County Circuit Court.
Prosecutors say text messages contradict their denial of an affair, a key point in a trial involving a former deputy police chief who claimed he was illegally fired.
Kilpatrick is the son of U.S. Rep. Carolyn Cheeks Kilpatrick, D-Mich.