Retail bosses are set to be hauled in for interviews this month in an investigation launched by the Competition and Markets Authority (CMA).
It is concerned fuel costs are higher than they should be and increases cannot all be blamed on global factors, such as the war in Ukraine.
Prices last year were on average of 5p-a-litre more expensive than they would have been had supermarkets maintained their average profit margins at 2019 levels, the CMA said.
Chief Executive Sarah Cardell warned that there was evidence weakening competition among retailers had pushed up fees for drivers.
There was evidence at least one company had increased its internal profit targets and others may have also have adjusted prices, she said.
The rocketing costs come despite Chancellor Jeremy Hunt confirming fuel duty would remain frozen for a thirteenth consecutive year, and extending the 5p-a-litre cut for another 12 months, during his budget in March.
Liberal Democrat MP Sarah Olney said it was “shocking” that there was evidence at least one company had inflated prices to “profiteer off the cost of living crisis”.
“This supermarket must be named and shamed,” she said. The Government has completely failed to bring down prices and have been ignoring allegations of profiteering for far too long.”
Ms Cardell told BBC Radio 4: "We are concerned about this increase in retailer margins and it doesn't appear to be driven entirely by factors outside of retailers' control.
"Obviously things like the war in Ukraine have had a significant impact on pump prices, but we have identified for example at least one supermarket has increased its own internal targets for its margins and we know that other supermarkets are aware of that and may have adjusted their own pricing behaviour accordingly.
"So we are calling in the representatives from the supermarkets for interviews over the next couple of weeks.”
She added that diesel margins have remained “significantly higher" than petrol and it is “not clear why that is".
The CMA will also look at the grocery retail market as food costs continue to rise.
Ms Cardell said: “Grocery and food shopping are essential purchases. We recognise that global factors are behind many of the grocery price increases, and we have seen no evidence at this stage of specific competition problems.
“But, given ongoing concerns about high prices, we are stepping up our work in the grocery sector to help ensure competition is working well and people can exercise choice with confidence.”