The 44-year-old is accused of having assaulted his father in March, Australian media report. He has been charged with domestic violence common assault as well as stalking and intimidation.
He has denied the allegations, telling broadcaster ABC they were “not true at all”.
Footage from the mass shooting at an event to mark Hanukkah showed Ahmed wrestling a gun from one of the alleged attackers.
He was shot several times in the process and subsequently visited by Australian Prime Minister Anthony Albanese in hospital, who called him the “best of our country”.
A fundraiser to support him raised more than A$2.5m (£1.24m; $1.7m).
Ahmed is due to appear in Sydney’s Bankstown Local Court on 29 June.