Immigration New Zealand's modelling data, which uses age, gender and ethnicity of immigrants to identify likely troublemakers is a "clear breach" of the law, the Green Party says.
Immigration Minister Iain Lees-Galloway said he found out about the programme only this morning when he was contacted by Radio New Zealand.
The data profiling is used to identify groups that most commonly run up hospital costs or commit crime so the agency could move faster to deport them rather than prosecute or allowing them to reapply for visas.
Green Party's immigration spokeswoman Golriz Ghahraman said she had written to the minister expressing concern about the programme.
"The use of identifiers such as race, age and gender in determining access to resource or opportunity is a clear breach of the New Zealand Human Rights Act," she said.
"The latest breach by Immigration NZ is heartbreaking. Immigrants are not data points in an algorithm, they are people who contribute to our communities and to our economy."
The New Zealand Association for Migration and Investment said the programme is tantamount to accusing all migrants irrespective of their country of origin.
"This approach appears to be another way of reducing migrant numbers ... an individual will be deported or refused entry due to their background being similar according to computer profiling rather than actual facts," said association chair June Ranson.
"This process is hypocritical when our Government has previously criticised Australia for doing the same thing."
Ranson said declining a visa or deporting someone based upon a statistical likelihood they may offend was unfair and a breach of natural justice.
"Our main concern is if statistical data is used to assess the 'genuine and stable' nature of a relationship in partnership-based applications," she said.
"We believe this could critically undermine the applicants' and their NZ partners' rights in the protection of their family unit and that is something protected by international law."
The association said it had seen an increase in declines for these applications.
INZ said the programme was a pilot which had been operating for the past 18 months.
Lees-Galloway said officials had assured him that it wasn't racial profiling and a range of data was being considered.
He had requested a full briefing from immigration officials.