As an award-winning journalist on Australia's premier current affairs program, Louise Milligan is used to tackling difficult stories and upsetting people in power, but her three-year investigation into allegations of child sexual abuse against George Pell, the country's most senior Catholic, was daunting.

Louise Milligan is an investigative journalist with Four Corners. ( ABC News )

"Without a doubt this is the toughest story I have ever done," Milligan said.

"This is a person who had immense political and cultural power so taking that on is enormous and very, very stressful. "Being at the centre of this storm, it doesn't get any harder than that as a journalist.

"Having said that, it pales into comparison with what this ordeal has been like for the people who made complaints about George Pell, and their families."

On Four Corners, Milligan secured exclusive interviews with the family of a choirboy, (who died of a heroin overdose), that Pell has been convicted of abusing on one occasion at St Patrick's Cathedral in 1996.

Pell has denied the offence took place and is appealing his conviction.

The boy was 13 years old when he was abused by George Pell. ( Supplied )

Milligan was the first journalist to report the allegations, very briefly in a story for 7.30 in 2016 and in detail in her book: Cardinal, The Rise and Fall of George Pell.

"I first spoke to the mother and sister in 2016 and it was obviously a very, very big thing for them to speak to us because they had never really told anyone how their son had died," she said.

"But they made the decision to speak out to support the other complainants.

"For legal reasons we weren't able to broadcast the interview at the time, but I referred to the allegations in a piece-to-camera.

"I asked the mother if it was OK if I told the story, de-identified, in my book and that was the first time anyone had really heard the story of the choirboys.

"After the first edition was published the father contacted me and told me he wanted to tell more of the story, which we hear in [the] Four Corners program."

Milligan has also previously spoken to the choirboy whose evidence convicted Pell, however he remains fiercely protective of his privacy and unwilling to speak publicly about the case.

Milligan's 7.30 story won two Quill awards from the Melbourne Press Club, including the Gold Quill for best story of the year, and her book was awarded the 2017 Walkley Book Award and the Sir Owen Dixon Chambers Law Reporter of the Year Award.

"When this story first came to my attention with the Herald Sun front page story about a police investigation into Pell, I just didn't believe it," recalls Milligan.

"It wasn't sourced, there was no-one quoted and I was highly sceptical.

"So I came to it with an open mind.

"Reporting on this story has been an enormous amount of work.

"Everything has to be very carefully fact checked, there's been so much research and it's legally very challenging territory.

"Every word, every story had to be very carefully thought through.

"It has been exhausting but it's been a privilege."

Milligan went from reporting on the Pell story to being front and centre when she was called as a witness during the committal hearing and spent six-and-half hours being cross-examined by Pell's barrister, Robert Richter, an experience she says has given her an insight into how brutal the legal process can be.

"That was extraordinarily stressful," she said.

"It was strange being in the court room and having my peers listening and reporting on me.

"I felt my words were being twisted, I was accused of flirting with a man who had disclosed his alleged abuse to me, which the magistrate slapped down, and the barrister withdrew it.

"I felt this huge responsibility to the complainants who had come forward to me to not let them down.

"The thing that stood out to me was that we'd just had this royal commission talking about how we needed a better approach in the criminal justice system to dealing with these types of proceedings and I felt like it was 1985 and it had all been ignored.

"I have a law degree, I have reported on courts for two decades, I had an amazing QC representing me, the ABC behind me and I found it traumatic and all I could think about was what it would be like for the surviving choir boy or other complainants giving evidence."

While it has been enormously difficult at times, Milligan says she felt compelled to stay with the story for the sake of those she has met who have felt abused and failed by the church.

"The layers and layers of sadness I saw drove me," she said.

"Seeing what had happened to a whole community where there'd been widespread abuse and the way the Catholic Church dealt with it.

"It's an appalling history.

"This is not about vindication, this is about the little kids whose lives were destroyed and whose families were left to pick up the pieces and I still feel enormously sad about it."

Watch Louise Milligan's investigation, Guilty, on Four Corners on iview.