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.

There has been significant internal squabbling at AFIC since allegations surfaced in 2015 that some of its schools were operating at a profit and sending money back to the parent organisation.

Mr Trad had served as AFIC president since late 2016, and made headlines in February when he claimed in an interview on Sky News the Koran states it is OK for a husband to beat his wife, but only as a last resort.

He later described that statement as "clumsy".

The internal disputes at AFIC became so acrimonious that in February ousted leaders seized the headquarters and bank accounts in a dramatic coup and the matter ended up in court.

Haset Sali helped found AFIC more than 40 years ago.

"The tragedy with AFIC is that it's a little bit like the Titanic, shuffling chairs while chaos reigned," he said.

"I can't see [the new president] as being an improvement on Keysar Trad."

Mr Sali said he was so worried about AFIC's direction he wrote to the Federal Education Minister Simon Birmingham and the NSW Premier Gladys Berejiklian, urging them to appoint an administrator.