The Townsville aquarium, also known as Reef HQ, has been home to a reef education centre and a living coral reef.
The funding, announced on Friday, takes the total committed by the government to $180 million and will allow work to begin to rebuild the facility, which was opened in 1987 by then Labor prime minister Bob Hawke.
The investment means the Great Barrier Reef Marine Park Authority will have a new purpose-built facility for reef education and be able to provide immersive experiences attracting domestic and international visitors, the government said.
"Like Bob, we want to create the Great Barrier Reef on land, making the reef accessible and affordable while spreading the reef conservation message and inspiring action to protect this spectacular natural icon," Prime Minister Anthony Albanese said in a statement.
"This funding announcement is an investment in the future of our precious Great Barrier Reef."
The project is expected to create more than one thousand jobs and give Townsville an economic boost worth millions of dollars.
Mr Albanese is in Townsville on Friday to attend The Courier Mail Bush Summit, alongside his state counterpart Steven Miles and federal Opposition Leader Peter Dutton.
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