An internal INZ investigation has since identified 459 more applications that may have been wrongly declined since July 2011.
The battle for a partner's visa has taken an emotional toll on Manisha Bhatia, 25, who been separated from her husband for more than a year after two applications were declined.
"Sometimes it's become very difficult for us to handle the situation - emotionally it's very disastrous."
A trained physiotherapist, Ms Bhatia moved from India to Hamilton in July last year to undertake a graduate diploma in sport and exercise science at Wintec.
The course, costing more than $20,000, was at a level that would enable her husband Naresh Kumar, 33, to apply for a spouse's visa to support her while she studied.
But two months after she moved to New Zealand, her husband's visa but was declined on the grounds that their relationship was not genuine.
Ms Bhatia applied again, this time with documentation to prove she and her husband had lived together for six months after their marriage in December 2011 - but the application was declined again.
Her husband also applied for a visitor's visa to see her, but even that was declined.
"That was the most frustrating point - it's something like it's a punishment. You have come here and you have to live here alone."
INZ has now written to inform Ms Bhatia that her case was eligible for reassessment - but has told her the file would not be reopened because she had applied for a visa for a third time.
Ms Bhatia is now seeking a refund of her first two visa application fees, which had cost about $200 each.
She graduated this year and can remain in New Zealand on a job search visa until next July. She is hoping her husband can join her before then.
The complaints to the Ombudsman were made by immigration advisers and New Zealand's leading professional association for immigration specialists, the New Zealand Association for Migration and Investment (NZAMI).
Association chairman Walter Stone said the initial assessments in India were very badly handled.
"They show a lack of training and bias. This reflects poorly on Immigration New Zealand."
He said partners applying through the Indian branches had been declined at much higher rates than through other branches, including China.
"It is precisely this inconsistent and poor decision-making that impacts very negatively on the reputation of New Zealand as a migrant destination - not to mention the cost to taxpayers of reopening over 480 cases."
Mr Stone said allowing partners to live with international students - who contributed 28,000 jobs and $2.6 billion a year to the economy - was a great way for the education sector to market its courses overseas.
He said many international students went on to contribute to New Zealand by getting skilled employment and working their way to becoming residents.
INZ area manager Michael Carley said it had contacted all potentially affected applicants and informed them if they were eligible for reassessment.
"A dedicated team of immigration officers not involved in any previous decisions relating to the cases has begun the reassessment process.
"INZ would like to apologise for this error and wants to reassure affected customers that their applications will be reassessed as a matter of priority by dedicated specialists in our Indian offices.
"Extra staff training has taken place in India following this case. We place huge importance on our customer service and we are confident that these changes will result in a big improvement."
