Parts of the Sunshine Coast and national parks at Moreton and Bribie islands, north of the state capital of Brisbane, were declared disaster zones.
A team of 130 specialists have been deployed to clean up the area.
Environment experts said the clean-up would be difficult as cyclonic seas and high tides continued to erode beaches, washing the spill into nearby rivers.
Radar-equipped aircraft were searching for the missing fertiliser containers, which could cause harmful algal blooms, suffocate fish and kill natural habitats.
A dozen sick animals have been discovered and the environmental protection authority says the number is likely to rise.
Anna Bligh, the premier of Queensland, said: "If there is any ground for prosecution of this ship and its owners, we will not hesitate to take that action. We will also be pursuing them for compensation as this is going to be a very big clean-up."
The ship's owners, Swire Shipping, faces $977,000 in fines if found guilty of environmental or maritime breaches.
The Sunshine Coast is one of Australia's most popular tourist destinations with several major resort towns located not far from the spill area.
The region is home to a range of sea birds and other creatures, including turtles, dolphins and pelicans.