Federal Transport Minister John Anderson ordered an immediate review of maritime security, the Australian Broadcasting Company reported.
He said the worst case scenario would be for a hijacked ship full of explosives to be detonated somewhere near a high-value target like the waterside Sydney Opera House.
He said he is also concerned about the potential threat from gas and oil tankers and ships carrying fertilizer.
He said there are a "surprising number" of potential dangers linked to ships that traverse Australia's harbors.
Under laws passed last year, about 300 port facilities will have their own security plans in place by July.
Lachlan Payne, speaking for the Ship Owners Association, said the industry will cooperate and the review should have happened much earlier.