The US president launched an attack on both nations for breaching the agreement, saying "they don't know what the f*** they are doing" on live television.
His comments came after Israel accused Iran of breaking the truce.
But Mr Trump lashed Israel for the number of bombs he claimed it dropped between the deal being made and the ceasefire taking effect.
Treasurer Jim Chalmers said Australians shouldn't be concerned about the words used.
"Far be it from for Australians to quibble with that kind of language," he told Sky News on Wednesday.
"We heard some blunt speak from the president, and I think that just reflects the fact that the stakes are high in the Middle East.
"I think those who haven't used that word privately can cast the first stone."
Nationals Senator Matt Canavan had a light-hearted take on the president's outburst.
"Ultimately, it's better that F-bombs are dropped than real bombs, isn't it? So let's hope this ceasefire does hold," he told Nine's Today show.
Meanwhile, a Royal Australian Air Force jet carrying more than 100 Australians trying to escape the conflict in the Middle East, has flown out of Israel after airspace was reopened.
Speaking from the NATO summit at The Hague, Defence Minister Richard Marles confirmed the 119 passengers left Tel Aviv in the early hours of Wednesday.
"We were very pleased to be able to provide that flight, and they've now been relocated to a place within the region, which is obviously outside of the danger zone," he told reporters.
"We continue to have (military) assets in the region ready to be able to provide assistance."
Mr Marles said the government had also chartered civilian aircraft for future departures "in certain circumstances".
The evacuees were taken out in a KC-30 RAAF jet.
There are still about 3000 Australians in Iran who've registered with the government for help to leave, and more than 1000 in Israel.Â
Foreign Minister Penny Wong said assisted departure flights from Iran were still not possible.
The latest conflict erupted on June 13, when Israel fired missiles at Iran in a bid to blow up military assets, arguing it was on the cusp of developing nuclear weapons.
The battle took a turn on the weekend when the US launched a bombing raid on Iran, blowing up three underground nuclear facilities.
The airspace in both countries was shut to passenger aircraft, leading to the evacuation of Australian embassy staff and their dependents from Tehran.
But the current ceasefire has not calmed the fears of Iranians in Australia.
The Australian-Iranian community lives in fear of US or Israeli bombs killing their friends and family while also worrying about the threat posed by Iran's autocratic Islamic government to their loved ones.
Persian Australian Community Association member Nader Ranjbar, there was hope the conflict could help de-stabilise the Iranian autocracy and pave the way for a new, democratic government.
Without a new regime, he is concerned that the current administration will intensify its persecution of the Iranian people.
"That's my worst fear," he told AAP.
"That somehow they get away from this mess and the first thing they do is start killing Iranian people."
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