It is a rare thing to see a judge step into the witness box, pick up the Bible and swear to tell "the whole truth and nothing but the truth".

It is even more unusual to see them then admit that they got something wrong.

But that is what NSW District Court Judge Gary Neilson did on Monday morning.

Well, sort of.

More than a year after he shocked the legal fraternity and the broader community by saying that incest was no less "unnatural" than homosexuality, Judge Neilson has conceded that some of his comments were "unfortunate" and unnecessary, while others were "misinterpreted".

However, on Tuesday his barrister will argue that the complaint against him should be dropped.

"I'm not a politician, but clearly incest breaks up families," said the highly experienced judge, looking somewhat out of place in a charcoal suit rather than his wig or gown.

"I suspect that is why it's maintained as a crime."

Judge Neilson was stood down from hearing criminal matters and referred to the Judicial Commission last year after he expressed the opinion that the community may no longer see sexual contact between siblings, as well as between adults and children, as "unnatural" or "taboo".

He made the comments during the case of a 58-year-old man who was charged with repeatedly raping his younger sister in the family's western Sydney home in 1981.

They were part of his justification for refusing to allow the jury in the case to be told that the accused, known as "MRM", had earlier pleaded guilty to sexually assaulting his sister in the early 1970s.

The comments included the opinion that, just as gay sex was socially unacceptable and criminal in the 1950s and 1960s but was now widely accepted, "a jury might find nothing untoward in the advance of a brother towards his sister once she had sexually matured, had sexual relationships with other men and was now 'available', not having [a] sexual partner".

He also said the "only reason" that incest was still a crime was because of the high risk of genetic abnormalities in children born from consanguineous relationships "but even that falls away to an extent [because] there is such ease of contraception and readily access to abortion".

The Court of Criminal Appeal overturned the decision to refuse the evidence.

On Monday, Judge Neilson  conceded that there was "absolutely no need" for him to publicly ruminate on why incest was a crime.

"No, there was nothing – I was just thinking out loud," the judge said.

"I always approach law on a historical basis – going back to obtain principles. But there was no reason to go back and consider why incest had been criminalised."

"Do you think incest is immoral," counsel for the judge, Phillip Boulten, SC, asked.

"I do," he said.

"Do you think it should be criminal?"  Mr Boulten continued.

"Yes, I do," Judge Neilson replied."

But he denied comparing incest and paedophilia to homosexuality on the grounds that, like homosexuality, they were no longer considered unnatural or taboo by the community.

The judge claimed that he had actually meant was that while juries had once considered sex between a man and his sister, or between an adult and a child "implausible" and "rare", they now accepted that this type of activity took place.

"It's been a mortifying experience to read the way it's been interpreted," Judge Neilson said.

"I accept that my attempt to convey that was extremely poor."

Counsel assisting the commission, Philip Strickland, SC, put it to the judge that an "ordinary, reasonable reader" of his comments would be interpret them as meaning that he did not believe that incest "abnormal, abhorrent or strange".

After initially denying this, the Judge conceded that it "could" be interpreted in such a way, and that this could tend to undermine faith in the judiciary.

The parties will move to closing submissions on Tuesday, with Mr Boulten indicating that he will argue  that the complaint against his client should be dropped.