The two leaders were speaking to discuss a deal made in the last days of the Obama administration that would see the US take in 1,250 refugees from Australia's offshore detention network.
"This is the worst deal ever," Trump reportedly said, before accusing the Australian prime minister of attempting to export "the next Boston bombers".
When Turnbull attempted to change the topic to the conflict in Syria, Trump reportedly ended the call.
In an interview on 2GB radio on Thursday afternoon, Turnbull denied Trump had hung up on him.
"This is not a deal that [Trump] would have done or that he would regard as a good deal," he said. "But it is one he has committed to."