The end of the fuel excise discount will hit millions of motorists, while consumers may face the added impact of higher food prices due to increased transport costs.
Fuel taxes were reduced by 32c a litre from the start of April in response to soaring oil prices due to the conflict in Iran.
The discount was wound back to 16c from the start of July, before ending altogether after Sunday.
While the latest price increases could take time to filter through to bowsers, petrol costs have already risen by an average of more than 40c a litre since the end of June.
Diesel prices have soared by more than 60c a litre in most capital cities over the same period, which has coincided with breakdowns in a ceasefire between Iran and the US.
Treasurer Jim Chalmers has written to the Australian Competition and Consumer Commission asking for increased scrutiny of fuel prices to ensure they weren't being artificially inflated at the expense of motorists.
"Servos and suppliers are on notice - the regulator will be watching them like a hawk," he said, adding that the fuel excise discount had "helped take the sting out of petrol prices at their peak".
Returning the fuel excise to normal was an unfortunate but fiscally necessary measure, Health Minister Mark Butler said on Sunday.
"We've got to get back to a situation normal at some point," he said.
But the excise, along with a return to regular road user charges for heavy vehicles, are expected to have flow-on effects for the food and agricultural sectors.
The unpredictable, "on and off" conflict in the Middle East made it hard for suppliers to make decisions, Independent Food Distributors Australia chief executive Richard Forbes told AAP.
"If the volatility continues and the price of fuel continues to rise, then it will be very difficult for businesses to plan how it will affect them," he said.
While food supplies were not under threat in most regional and metropolitan areas, trucking and food companies would likely need to pass costs on, Mr Forbes added.
Australian Livestock and Rural Transporters Associations' chief executive Ben Maguire said his members were not worried about price rises, they were worried about being unable to work altogether.
Some truck drivers had reported downing tools in anticipation of diesel costs rising because their customers could not afford to pay higher prices.
“It’s not just about getting food to consumers, it’s about actually being able to grow food," he said.
“The transport industry is already under stress. They are resilient people, but we shouldn't be living, in a nation like Australia, where a whole sector doesn't know where the next dollar is coming from."
Herbicides, fertiliser and diesel needed to be moved onto farms at affordable rates to prepare for the coming season, or agricultural production would not be able to continue at its normal rate, Mr Maguire added.
