AFIC has nine Islamic councils and dozens of smaller affiliates as members. It spends its funds on a range of activities, including grants to Islamic societies and donations to individual imams around Australia.

Chief executive officer Amjad Mehboob.

On 25 March 2006 The Australian reported that a report prepared for AFIC by "forensic accountant Robert Smith" claimed the Council was funnelling money from a non-profit school to fund its other activities. The story, written by Natalie O'Brien, said the school received more public funds than any other in NSW and $11 million from the Federal Government. The school's rent, cleaning and accounting fees made up two thirds of AFIC's budget. Mr Mehboob was reported as saying that Mr Smith had got it wrong.

Richard Kerbaj, writing in The Australian of 4 April 2006, said the NSW Muslim Council proposed to call for the position of Mufti of Australia to be made vacant as part of a plan to set up a national board of imams identified by the executive of the umbrella body the Australian Federation of Islamic Councils.