It is understood the 79-year-old died in hospital on Monday night after battling pneumonia and kidney disease.
McIntosh was a teacher and tutor at Dilworth School during the 1970s. He is believed to have left in the late 1970s and moved north where he taught at Ruawai College where allegations of sexual abuse surfaced after it became public knowledge he was gay.
His death follows that of Richard Charles Galloway, another one of the nine men who have been charged as part of Operation Beverley, the investigation into historical sexual abuse at Dilworth School.
Galloway died on November 26 aged 69 after earlier being diagnosed with cancer.
In March, former Dilworth house and scout master Ian Wilson was sentenced to three years and seven months in prison for indecently assaulting five students between 1975 and 1992.
The 69-year-old said through his lawyer during sentencing that he was remorseful for his actions, but was introduced to "degenerate" behaviour at the school.
"He was approached by a staff member who introduced him to a mode of behaviour at the school that was degenerate, and he fell under the spell, but that is in no way an excuse and he accepts and acknowledges that."
Five men are still going through the court system, including Ross Browne and Alister Harlow.
Others have been granted name suppression.
Two men are due to appear at the High Court in Auckland on Wednesday.
More than 100 victims have now emerged in the Dilworth School sexual abuse investigation. There were two new arrests today.
After the initial arrests in September, police were swamped with calls from other men who also wanted to report allegations of abuse.
Where to get help:
• If it's an emergency and you feel that you or someone else is at risk, call 111. • If you've ever experienced sexual assault or abuse and need to talk to someone call the confidential crisis helpline Safe to Talk on: 0800 044 334 or text 4334. (available 24/7) • Male Survivors Aotearoa offers a range of confidential support at centres across New Zealand - find your closest one here. • Mosaic - Tiaki Tangata: 0800 94 22 94 (available 11am - 8pm) • Alternatively contact your local police station • If you have been abused, remember it's not your fault.