The federal government announced the measure, in consultation with Fertilizer Australia, as the Middle East conflict continues to put pressure on fertiliser and fuel supplies.
Sixty per cent of the supply of urea to Australia for fertiliser travels through the Strait of Hormuz, which has remained closed since US-Israeli strikes launched on Iran in February.
Agriculture Minister Julie Collins said the changes would reduce costs, reduce port clearance times, lower administrative burdens and ensure the safety of fertiliser prior to shipping.
She said strict biosecurity standards will not be impacted.
"There's enough fertiliser in Australia today and on its way on the water in terms of the initial planting season," Ms Collins told Sky News on Thursday.
"But this is about longer term supplies because of the unpredictability and we don't know how long this is going to go."
The changes include certification from an authorised inspector offshore that the goods are free of biosecurity risk for all imports and a requirement for importers using higher-risk pathways to provide a bagged sample for prior inspection.
Meanwhile, an unprecedented fire broke out in Geelong at one of Australia's two operational oil refineries on Wednesday night.
The refinery produces 50 per cent of Victoria's fuel and 10 per cent of Australia's.
Energy Minister Chris Bowen said fuel supplies would be impacted as the blaze continues to burn out of control.
Trade Minister Don Farrell is travelling to Singapore on Thursday to join Foreign Minister Penny Wong in a bid to guarantee ongoing fuel supplies.
"The government has prioritised Southeast Asia, and it is more important than ever that we work closely with our neighbours," he said.
"We know that the impacts of this conflict will be with us for some time, and we are taking every practical step to secure what Australians need to keep our country moving."
It follows Prime Minister Anthony Albanese's visit to Singapore last week, where he agreed on strengthening energy ties with his counterpart Lawrence Wong.
Singapore provided 26 per cent of Australia's refined fuel imports in 2025, while Australia was the source of 32 per cent by volume of Singapore's LNG imports.
Mr Albanese is in Malaysia where he continues his string of international visits to shore up Australia's fuel supplies.
Malaysia supplies 14 per cent of Australia's diesel, 10 per cent of its petrol and 11 per cent of its jet fuel, and is also the nation's largest provider of crude oil.
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