The Museum's Pyrmont Bay wharves need urgent repairs due to a small mollusc known as a shipworm, which has been eating away at its historic wooden pylons.
The budget has allocated $10.1 million over two years for the much-loved Sydney institution to carry out urgent remediation work.
Sometimes called the "termites of the sea", the shipworms have munched through many of the 320 pylons under the Museum's wharves, creating a honeycomb of tunnels that undermines their structure.
The funding will fix piles under wharf seven first, followed by the north and south wharves, by wrapping the structures in steel.
Most of the work is expected to be finished within 12 months.
According to the publication Shipwrecks and Global "Worming", shipworms have been responsible for destroying boats since ancient times.
They were arguably part of the reason England defeated the Spanish Armada in 1588, having weakened the hulls of the Spanish fleet so they were unable to withstand English cannonballs, as well as UK weather.
Since these creatures thrive on clean salt water, better water quality at Sydney Harbour has meant an increase in a variety of small marine creatures, including oysters, that have wreaked havoc on the wharves.
As for the museum, wharf seven is no longer strong enough for vessels to be moored against it, and the lightship Carpentaria as well as the tall ship James Craig had to be moved.
The budget money means the museum will not have to draw from its regular operational funding to carry out repairs.
"This extra funding ensures the safety of our wharfs and keeps our world-famous vessels and collection secure and available to visitors," museum director and chief executive Daryl Karp said.
Mr Karp is keen to reassure people that the museum is safe to visit, with affected areas closed off.
The money is one of very few new federal budget measures aimed at the cultural sector, with overall spending at $1.1 billion for 2026-27 including modest increases for funding body Creative Australia.
It's not enough for a struggling sector, according to lobby group Save Our Arts, especially with household budgets under pressure.
"The cultural economy is particularly vulnerable to spending reductions and needs help through this period," campaign director David Latham said.
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