The two nations on Wednesday signed a memorandum of understanding (MoU) to more quickly develop new fuels and digitise port clearance, port calls and the flow of vessels.
"This is an important partnership for a sustainable global maritime future," Transport Minister Catherine King said.
Australia could become a key producer of green marine fuels hydrogen and ammonia for the world's busiest port under the "green shipping corridor" pact.
"This collaboration will place Singapore and Australia amongst the leaders in contributing to the international maritime community's objectives, while supporting Australia's exports of clean renewable energy," she said.
CSIRO is already working with the city-state's scientists on demonstration projects and pilots under a low-emissions technologies program for maritime and port operations.
Singapore's Minister for Transport Chee Hong Tat said the two countries would share expertise and resources, and upskill the workforce to support the energy transition.
The international shipping industry, which transports most of the world's goods, is under mounting pressure to end its reliance on fossil fuels.
If shipping were a nation it would be the eighth-largest emitter in the world, according to the International Maritime Organisation.
Further, the shipping industry's three per cent of global emissions could increase to 10 per cent by 2050 without stringent measures.
The sector has set a target of net-zero emissions "by or around" 2050 but it's a tough challenge with a hefty price tag and no alternative fuels ready to ship.
Other leading trading nations have also pledged to develop green shipping corridors - including the US, the UK, Norway, Korea and Japan - to reduce the toll on the environment.
But emissions-reduction operations at sea and at ports, assessing routes, alternative fuel use and bunkering, and infrastructure requirements for new fuels need to be understood.
Australia's formal bilateral agreement at the leaders' meeting in Melbourne builds on a green economy pact struck in 2022.
Under the MoU, both countries will work with industry on fuel supply chains for the maritime industry, including building infrastructure, formalising standards, and developing and implementing new training.
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