The apparent disagreement was over an exchange of refugees agreed between Australia and the Obama administration late last year.
On Twitter, the US President said he would “study this dumb deal”.
Under the terms, the US would re-settle up to 1,250 asylum seekers, most of whom are held in processing camps on the Pacific islands of Nauru and Papua New Guinea.
In return, Australia would take refugees from El Salvador, Guatemala and Honduras.
But during Mr Trump’s weekend conversation with Australian Prime Minister Malcolm Turnbull, the US President is reported to have described the refugee agreement as “the worst deal ever”.
According to The Washington Post, he also accused Mr Turnbull of trying to export the “next Boston bombers”, referring to Tamerlan and Dhozkar Tsarnaev, Russia-born US citizens who set off two bombs at the 2013 Boston marathon.
Three people were killed in the blast and more than 260 injured.
Mr Trump reportedly told Mr Turnbull: “I don’t want these people.”
He is also reported to have said that he had spoken to four world leaders that day and “this is the worst call by far”.
He is reported to have told Mr Turnbull that it was “my intention” to honour the deal, words that would leave him room to back out