With global oil prices surging, diesel suppliers are prioritising long-term contracts and holding back extra fuel, reducing availability on the spot market.
Many Australian farmers rely on ad hoc deliveries rather than long-term contracts, leaving some struggling to secure fuel at predictable prices.
Some say disruptions could impact production and transport, driving up prices for consumers.
Cattle grazier John Lowe said the uncertainties had come at a terrible time for many producers as diesel prices in some regions jumped about 40c per litre.
Many farmers were reporting fuel deliveries becoming harder to secure, while prices surged.
In one case cited by Mr Lowe, a producer locked in a delivery of about 27,000 litres at $1.70 a litre, only to be later told the price had jumped above $2.
"The dry summer meant a lot of people were deferring their costs for as long as possible, which has made this a bit of a perfect storm," the NSW Farmers committee chair told AAP.
"As we started getting a bit of rain in the farming belt, we got this supply problem at exactly the same time."
Mr Lowe, who runs a cattle breeding and grazing operation in the NSW Central Tablelands, said the uncertainty had already disrupted his planning.
"The crops we thought we were going to plant, we may not get to plant," he said, adding it would have a flow-on effect on cattle grazing.
"We'll have to have a pretty big heart-to-heart with our bankers."
Fuel retailers say the disruption has been driven partly by panic buying and efforts among wholesalers to prioritise existing contracts.
"Unfortunately, there has been some panic buying of diesel which has depleted stock in some areas; however, these sites have been quickly replenished," Australian Convenience and Petroleum Marketers Association chief executive Rowan Lee told AAP.
The federal government insists Australia's fuel security remains strong.
Energy Minister Chris Bowen said the country remained above its minimum fuel stockholding levels and warned companies against exploiting the crisis.
"Australia's fuel pricing follows global markets, but the government has been clear - this is an international crisis, not a commercial opportunity," he said.
He cautioned industry to ensure farmers and smaller businesses could access the fuel they need.
But Nationals leader David Littleproud said farmers were already struggling to secure forward fuel contracts at agreed prices and obtain supply quotes.
"Farmers cannot get the fuel they need in regional and rural areas right now, which is placing enormous pressure on the agriculture industry," he said.
Retailers were yet to report shortages or supply-chain issues, an Australian Retail Council spokesperson told AAP, with any impacts likely to appear over the longer-term.
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