Keysar Trad, who said men should only hit women as a "last resort", has been dumped as the president of the Australian Federation of Islamic Councils (AFIC).
At an emergency meeting in Sydney on Saturday morning, Mr Trad was replaced by Rateb Jneid.
AFIC represents Muslims in Australia and is responsible for several Islamic schools. It also has the power to grant halal certification.
It had been ordered to hold fresh elections by the New South Wales Supreme Court after a messy internal dispute.