The three-month cut to the fuel excise started in April in response to soaring prices caused by the US-Israeli-led war on Iran and will run out at the end of June.
Prime Minister Anthony Albanese has neither ruled out nor confirmed he will extend the measure, which has reduced the cost of petrol and diesel by 26.3 cents a litre.
"(Mr Albanese) has made clear that obviously we will continue to monitor the situation," Mr Bowen told reporters on Saturday.
"But the excise was a temporary measure and we envisage it being a temporary measure."
There was no money in the May 12 federal budget to extend the excise, but it did include $3.2 billion for a new government-controlled fuel reserve.
The three-month excise cut has cost the federal budget $2.9 billion.
In a regular update on Australia's fuel stocks, Mr Bowen said an extra 50 million litres of diesel had been secured as a buffer for Western Australia.
There was also an additional 50 million litres of jet fuel to the nation's stocks amid "concern internationally" about jet fuel levels, Mr Bowen said.
It comes after the government on Tuesday announced extra jet fuel shipments of about 100 million litres had been secured from China and would begin arriving in June.
As part of its fuel reserves, Australia has 43 days' supply of petrol, 31 days of jet fuel and 38 days of diesel.
The war in Iran has resulted in the closure of the Strait of Hormuz, through which one-fifth of the world's oil supply passes, and created volatility in global markets.
The Australian government wanted to see a resolution to the conflict but was not a central player, Mr Bowen said.
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