According to a tribunal decision in March this year, the offending took place 30 years ago and the man had not re-offended since, with letters from friends and family describing positive changes he has made since his release.
He was deemed at low risk both in terms of reoffending and the harm posed to his wife.
But Immigration New Zealand [INZ] said these factors were not compelling enough to grant the man a character waiver.
The offending was "extremely serious" given their sexual nature, the multiple victims, and the extended time over which it took place, INZ said.
The couple got to know each other online in January 2018 and met in person for the first time in the Philippines two months later, before marrying in July the same year.
She arrived in New Zealand on a visitor visa in May 2019 and has since filed several visa applications and follow-up appeals under the family [partnership] visa category.
All were declined because her husband was not eligible as a supporting partner due to his rape convictions.
INZ conducted two rounds of character waiver assessments for the husband, and in both cases was "unable to overlook the seriousness of the offences".
The man has worked continuously as a truck driver since 2006 and his employer described him as hard-working, loyal and trustworthy.
His counsellor said he suffered from stress and fear that his wife would be deported. He blamed himself for the predicament.
His convictions also meant he was unlikely to get a Filipino visa, which could physically separate the couple if she were deported.
The woman works as a health care assistant, "providing important care" at a time when New Zealand's health infrastructure is under strain in the Covid-19 pandemic, the tribunal said.
She held a qualification in marine transport, a certificate in caregiving and housekeeping and had partially completed an undergraduate nursing course.
Getting residency on her current job would be challenging because of income requirements, but she was on an essential skills work visa until November 2023 and could "explore further employment and career opportunities that could lead to residence," the tribunal said.
Her parents and siblings were in the Philippines; she had an aunt and cousins in New Zealand.
Supporting letters showed she was actively involved in the community here, including volunteering with the Philippine Consulate.
Tribunal member Louise Moor was satisfied the couple were in a genuine partnership but noted their age difference, and the fact they married after spending very little time together.
They had "long-term plans to live together in New Zealand and start a family", the man undergoing a vasectomy reversal in 2020, according to INZ.
On this point, the tribunal said it was not satisfied the man posed no risk to future children.
Moor agreed the woman qualified for residence on all counts apart from her husband, but found no special circumstances to warrant a ministerial exception in her case.
Forming a relationship with a New Zealander as an overseas national and temporary visa holder is not special, the tribunal member said.
Character requirements for those who support residence applications are meant to protect vulnerable migrants under the family [partnership] category.
"[S]upporting a partner for residence is a privilege rather than a right," the tribunal said.