Judge Jan Kelly, who heard the application in the Wellington District Court on Friday, confirmed she would not have allowed the dismissal under the other legislation, or the stay of proceedings.
"This is not a decision I have come to lightly because ... I acknowledge the complainant's interest in having this proceeding, but in my view this is one of those perhaps exceptional cases where the discretion to dismiss the charges under section 322 should be exercised," she said.
Crown lawyer Megan Paish opposed the dismissal application, noting the complainant had been working and engaging closely with police since coming forward, and that she had been "significantly affected".
The man was accused of several representative counts of rape and indecent assault against a girl under 12, and indecent assault against the same girl when she was aged 12-16.
The offences were alleged to have happened between 1975 and 1977, but the complainant only came forward to police in 2017 after speaking to a therapist.
Charges were laid against the man last year. He pleaded not guilty and elected trial by jury.
Judge Kelly's decision cited a Supreme Court case, H and the Queen, which tackled how to deal with dismissal application under the relevant section of legislation when the defendant was no longer a young person.
That case law supported consideration of a number of factors, those being the defendant's age at the time of the alleged offending, the length of the delay, whether the delay was unnecessarily or unduly long, the seriousness of the offending, public interest in proceeding with prosecution, any evidence of rehabilitation in the meantime, and prejudice to the defendant.
Judge Kelly said the allegations were "very serious", and that there was public interest in pursuing proceedings.
She also said no fault could be found in the complainant taking 40 years to report the matter to police.
"It is well established that there are often good reasons for delays in the reporting of historic sexual offending," she said.
"I do however consider that the time that has elapsed is unduly protracted from the perspective of the defendant."
Judge Kelly also noted while the man had a steady offending history for burglary, fraud, and other dishonesty offending until the mid 80s, he had no charges or convictions for sexual offending.
She also found the man's defence would be prejudiced if the case was to go ahead, with certain pieces of evidence difficult or impossible to gather after such a long time had passed.
With those factors considered, Judge Kelly granted the application for dismissal. While it was not "strictly necessary" for her to then consider the alternative applications, Judge Kelly indicated she would not have allowed the dismissal under the other pieces of legislation.
While the man did not have name suppression, he cannot now be named due to a last-minute suppression application being made following the dismissal hearing.
