An report by the Australian Senate Standing Committees on Economics in 2015 titled "Third party certification of food" found this allegation to be untrue since there was no evidence of halal certification fees being directly related to terrorism funding.
There have been various public claims that fees from certifying halal food
may be funding terrorism. AUSTRAC has no information that indicates
halal certification is linked to terrorism. AUSTRAC receives financial
transaction reports from businesses providing designated services under our
act. AUSTRAC monitoring of reported financial transactions allows
analysts to make judgements about potential risks of terrorism financing or
money laundering and refers relevant information to investigating agencies.
AUSTRAC monitors reported financial transactions, including reports of
suspicious financial activity and related transactions to identify money
movements associated with halal certification. Of the information identified
from this monitoring of reported financial transactions, none of these have
been assessed as being related to the funding of terrorism, with regard to
halal certification fees. AUSTRAC will continue to monitor reported
financial transactions and analyse data related to halal certification to
identify information that may be relevant to investigating agencies. Source: Third party certification of food.
Also a fact check by Australian Broadcasting Corporation found no evidence for directly linking terrorism and halal certification funds.
While the proceeds of halal certification do fund Islamic organisations, Fact Check could find no evidence that this money has ever flowed to terrorist groups. Source: Fact check: Does halal certification fund terrorism?