Mr Trump, who in March 2016 described his then-campaign aide as an "excellent guy", in November labelled him a "low-level volunteer" and "a liar".
The Trump campaign aides interviewed because of potential Russian ties included former national security adviser Michael Flynn, former campaign chairman Paul Manafort, and former foreign policy advisers Carter Page and George Papadopoulos, current and former officials told the Times.
The New York Times said top Australian officials broke diplomatic protocol to allow the agents to question the country's then-high commissioner to the United Kingdom previous year, with the results - summarised and sent to Washington on August 2 - laying the foundations for what was then known by its code name, Crossfire Hurricane, and is now special counsel Robert Mueller's probe.
"Within hours of opening an investigation into the Trump campaign's ties to Russian Federation in the summer of 2016, the FBI dispatched a pair of agents to London on a mission so secretive that all but a handful of officials were kept in the dark", the New York Times reported on Wednesday.
The FBI's Trump-Russia investigation had a secret codename based on a Rolling Stones song
'After tense deliberations between Washington and Canberra, top Australian officials broke with diplomatic protocol and allowed the ambassador, Alexander Downer, to sit for an Federal Bureau of Investigation interview to describe his meeting with the campaign adviser, George Papadopoulos'. "Their report helped provide the foundation for a case that, a year ago Thursday, became the special counsel investigation".
"Crossfire Hurricane", a reference to a Rolling Stones lyrics, continued in secret as Trump publicly railed against the investigation, calling it a "witch hunt".
Mr Papadopoulos became one of Mr Mueller's first scalps, pleading guilty to lying to officials.
He is co-operating with Mueller's investigation. According to the story, what was then known as "Crossfire Hurricane" amongst the handful of agents involved, began months before election day.