Agriculture Minister Tony Burke said in a statement that he had received it, and would take the time needed to thoroughly review it before making any decision on its recommendations.
No time for its public release has been given.
"It is my intention that the report will be publicly released once it has been considered by the Government," Burke said.
The inquiry, headed by retired High Court judge Ian Callinan, is expected to make wide-ranging recommendations aimed at strengthening quarantine measures, which are a federal responsibility in Australia.
The government is expected after its release to discuss future handling of imported horses with various equine industry sectors.
The report is also expected to provide a view on the most likely route by which the highly contagious virus escaped into the general horse population.
Industry groups are eagerly awaiting the report in the hope it will add weight to class actions against the government for losses resulting from the flu outbreak, which began last August.
At least one class action for 350 clients is reported to be ready to proceed once the inquiry report is made public.
Meanwhile, the agriculture minister has reminded interested parties they have until Monday to make a submission to the independent review of Australia's quarantine and biosecurity arrangements.
Burke announced the wide-ranging review in February and granted a two-month extension after a request by the head of the review, Roger Beale.
The report will be submitted to the minister by September 30.
The panel's terms of reference include examining the legal, administrative and institutional frameworks that underpin quarantine and biosecurity arrangements.