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 excise discount was wound back to 16c from the start of July, before ending altogether on Monday.
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.
"The ACCC has the powers that they need to fine ... servos and suppliers up to $100 million per offence, and so servos and suppliers are on notice," he told ABC's RN on Monday.
"The regulator will be watching them like a hawk, and they can't use the return to normal settings with the excise as cover for treating motorists as mugs."
Dr Chalmers said it wasn't the government's intention to reintroduce the discount on the fuel excise, which has wiped revenue from the budget's bottom line.
"Obviously, we keep all of our policies under review, particularly when there's this much uncertainty in the world. But it's not our intention to bring it back," he said.
Petrol prices have already risen by an average of more than 40c a litre since the end of June, while diesel has soared by more than 60c a litre in most capital cities over the same period.
It follows the fragile ceasefire between Iran and the United States breaking down as conflict between the two nations flares.
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.Â
"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 said.
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.
"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," he said.
Some truck drivers had reported downing tools in anticipation of diesel costs rising because their customers could not afford to pay higher prices.
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 said.
