[citation needed] The definition of Muslim according to AFIC member organisation, the Islamic Council of Western Australia]], is "any person who conforms to the teachings of the Qur'an and Ahli Sunnah and Jamma' and shall specifically exclude any person or organisation, professing adherence to the Ahmadi, Lahori, Qadiani or Baháʼí schools of thought or of any similar inclination".

[9] However it was reported in February 2017 that following a bid to take-over AFIC, which involved the changing of locks and the passing of no-confidence motions against the current executive, Trad has not been able to enter his office.

[11] Professor Shahjahan Khan, former vice-president of the Islamic Council of Queensland, has said that to save AFIC from "self-destruction", the younger generation of Muslims need to work to rebuild the organisation.

[2] In April 2021 it appointed Sheikh Abdul Quddoos Al-Azhari as new Grand Mufti of Australia, with the Australian National Imams Council, a rival Sunni organisation, objecting to this, as Ibrahim Abu Mohamed had held this position since 2011.

[13] On 9 March 2024 AFIC appointed Sheikh Riad El-Rifai as the Grand Mufti of Australia replacing Abdul Quddoos Al-Azhari.

[25][26] In 2012 a government audit discovered a number of irregularities relating to financial transfers between AFIC and its schools in Sydney, Brisbane, Canberra and Adelaide.

[29][23] In 2015, it was reported that there has been a long-running dispute between the Islamic College of Brisbane and the AFIC, which owns the land, has resulted in members of the school board and principal being dismissed or resigning.

[35][36] In mid November 2015 following a federal government audit, with the department concluding AFIC operates the schools for its own profit.

[46] In February 2017 the federal Minister for Education and Training, Simon Birmingham said the Islamic College of South Australia had failed meet obligations relating to governance, to financial management and to regular reporting.

[48] In March 2017 it was reported that, following a police request, in relation to the more than $1 million potentially missing and the high rentals paid to AFIC, the Australian Securities and Investments Commission have been undertaking financial investigations.

[54] In 2014 the founding president of the AFIC identified internal dysfunction and corruption as the cause of a long running feud within the organisation, which he says has disenfranchised Islamic councils around the country.

[56] Dr Jamal Rifi said that AFIC, as Australia's peak Muslim body, was "not capable of providing the leadership its communities need".

[11] In February 2017, in response to a question regarding the meaning of Quran Chapter 4, Surah 34, the president of the AFIC said a husband can beat his wife, but only as "a last resort".