The Australian Federation of Islamic Councils (AFIC) and the Islamic High Council of Australia on Friday appointed one of the country's longest-serving imams as National Grand Mufti of Australia.

However the role isn't exactly vacant.

Dr Ibrahim Abu Mohamad has been serving as Australia's Grand Mufti since 2011, with a short four-month break in 2018.

He was appointed by the Australian National Imams Council (ANIC), which has chosen a leader since AFIC retired the position almost 15 years ago.

AFIC first appointed a Grand Mufti in 1989 but scrapped the role in 2007 amid community concerns imams and muftis were distracted by "media fanfare".

"They (ANIC) jumped into that void. We don't believe that was the right thing to do," AFIC chief executive Keysar Trad told AAP.

Both bodies are now claiming only they can appoint a Grand Mufti.

AFIC says it is the peak body representing Muslims in Australia and by reviving the position, it hopes to unite the country's believers behind one leader again.

AFIC President Dr Jneid said Islamic society had suffered from "the division and the inadequate services from self-appointed leaders" and the new Grand Mufti would operate without favouring any group or nationality.

Its appointee - Imam Abdul Quddoos Al Azhari - holds a Diploma of Education and two Master's in Sharia and Arabic language, has been an imam and teacher for more than 40 years in Fiji, the Northern Territory and Queensland, and is fluent in several languages.

"Imam Quddoos, as we all know him, is a bundle of dynamite," Dr Jneid said, announcing the appointment.

"He spreads goodness wherever he goes ... tens of thousands of children, women and men continue to benefit directly from his efforts both in Australia and overseas."

AFIC had reached out to ANIC and asked Grand Mufti Mohamad to quit, Mr Trad said

"A number of our members have been talking to him and the other organisation about coming into the fold ... being part of the big picture."

"But the other side was not interested so we had to proceed in the best interest of the community."

But ANIC in turn said AFIC's announcement was a "surprise" as it isn't authorised to appoint a Grand Mufti.

As the role is inherently theological, that falls to ANIC which represents Australian-based Muslim clerics and imams across the country, spokesman Bilal Rauf says.

AFIC publicly stated as much in 2018.

ANIC has not been approached by AFIC and Grand Mufti Mohamad will not resign.

"As far as we're concerned, it is business as usual," he said.

He rejected suggestions the tussle would confuse everyday Muslims.

"It's unhelpful but it won't change the reality on the ground."

"I don't think there will be much confusion because they don't deal with AFIC, they deal with their local imams and there are in excess of 200 imams who are members of ANIC."

With neither party likely to back down, it seems Australian will continue to have two Grand Muftis.

As AFIC is the "peak" national body, Mr Trad says he hopes Imam Quddoos will be officially recognised as the true leader of Islam in Australia.

"We would expect the person that we appoint will take the leading role," he said.

But Mr Rauf said government and community have indicated "quite the contrary" and will continue to work with Grand Mufti Mohamad.

"For us, with Ramadan approaching, the focus is on giving spiritual and religoius instruction to the community.

"This issue is a bit of a sideshow, we won't let it distract us."

Australian Associated Press