Neville Joseph Creen, 80, denied indecently abusing the teenager in Mount Isa, northwest Queensland, where he served as a priest in the 1970s.

The alleged victim, who cannot be identified, first met Creen after his father was killed in a mining accident, crown prosecutor Katrina Overell told the Brisbane District Court.

Creen was accused of summoning the boy to his office and rubbing his thigh and groin on four separate occasions in 1974 and 1975. However, Judge Ian Dearden said much of the evidence was unreliable and self-contradictory.

"Although I'm prepared to accept that the complainant is seeking to give a narrative of events he believed occurred to him in 1974 and 1975 ... that narrative is completely unreliable, self-contradictory in places and cannot be accepted as evidence beyond reasonable doubt," he said during Friday's judge-only verdict.

"Other than in broad terms there is no objective or independent evidence that supports any aspect of the complaint's evidence in this trial."

After more than 40 years of silence, the alleged victim complained to police in 2016.

Asked about the allegations in 2018, Creen told officers he had "never, ever touched the boy", calling it a "gross injustice" that he had been accused.

"This is repulsive," Creen told detectives in the interview played to the court on Thursday.

"I think he's got the wrong bloke."

While there was an overlapping timeline of when Creen was a priest in Mt Isa and the boy's time at school, Judge Dearden said the "credibility and reliability" of the complainant were key.

Creen pleaded not guilty to four charges of indecent and sexual abuse at the start of the two-day trial, but one count was discontinued by the prosecution on Thursday.

There were significant inconsistencies in the accounts provided by the alleged victim and someone seemed to be giving him information to strengthen his case, defence barrister Debra Wardle told the court in closing.

She said the man also had a civil case against Creen which was a "powerful motivator".

But Ms Overell said the man was credible and "doing his best to tell the truth".

"Any inconsistencies are attributable to the passage of time and also the number of incidents he was attempting to recall," she added.

Creen was previously jailed for sex offences against young girls in the regional Queensland town between 1973 and 1981.

Australian Associated Press