According to figures provided under the Official Information Act, 51 institutions, including half of the country's polytechnics, have visa decline rates for Indian students of more than 30 per cent.
At most of the institutions more than half of applications are being turned down and at one the decline rate is 86 per cent, Radio New Zealand reported.
The figures covered the six months from the start of December 2015 to the end of May 2016 and were only for institutions with at least 10 visa applications from Indian students.
Immigration New Zealand said Insight programme that most of the declined applications in the first four months of this year were because it did not believe the applicant was really coming to study, or because it did not believe they had enough money to support themselves.
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In 2014, Immigration New Zealand warned New Zealand Qualifications Authority (NZQA) that high refusal rates could indicate problems with tertiary institutions.
Immigration said it had increased its audits of providers with high decline rates and was now assessing information obtained from the 10 establishments it had visited so far.
Auckland International Education Group spokesperson Paul Chalmers said the vast majority of the declined applications were not cases of fraud, but were simply not up to Immigration's specifications.
Immigration was sometimes turning down bona fide students, he said.
The international education spokesperson for the private sector body, Independent Tertiary Education, Richard Goodall, said immigration was being tougher on applications from India, but visa decline rates above 50 per cent were questionable.
"You're getting more declined than accepted, something's wrong along the way."
His organisation was one of 21 that Immigration New Zealand said had decline rates above 60 per cent.
"Some of it is a real necessary crack down on fraudulent activities and we support that. We have had rejections to student visa applications based on fraudulent activities. Working in Indian market you are going to be affected by that," Trivedi said.
Imperial College of New Zealand, which had the highest rate of refused applications at 86 per cent, did not comment on the report.