A 2-year-old New Zealand boy and his pregnant mother are facing the possibility of life without his dad after the Associate Immigration Minister went against an Immigration and Protection Tribunal (IPT) recommendation to grant residency.

Mother Annie Zhang, 32, is married to New Zealand citizen Douglas Chen, 57, but her visa application under the partnership category was declined by Immigration NZ (INZ) because Chen had previously successfully supported two previous applications.

They successfully appealed to the IPT, which found Chen had special circumstances to warrant a consideration as an exception to Government residence instructions by the Minister of Immigration.

But in a decision made on March 18 - the same day INZ announced visas for victims of the Christchurch mosque shootings would be fast-tracked - Associate Immigration Minister Kris Faafoi declined granting residency to Zhang.

Immigration lawyer Jack Tam, acting for the family, said the decision was "odd and irregular" because only once in the last 32 similar cases had the Minister gone against the findings of the tribunal.

"From precedents in the past, the minister defers to the tribunal and that's why we have a tribunal making objective assessments," Tam said.

"From what I can see, the one case that got declined previously was due to a health issue. There is no such issue here, so I do find the Minister's decision very odd and irregular."

A spokesman for Faafoi said the minister "does not comment on individual cases".

Zhang first met her husband at a friend's party in February 2015 when Chen was visiting China.

They stayed in touch through social messaging apps WeChat and WhatsApp, and Chen - a former Chinese national - made monthly visits to see Zhang.

The couple married in May 2016, and made plans for Zhang to move to New Zealand after they found out she was pregnant.

In August that year, she came to New Zealand on a visitor visa and gave birth to their son in April 2017. The son is a NZ citizen.

Supported by her husband, Zhang made an application for residence under the Family (Partnership) category in March 2018, but was told by INZ that Chen was not eligible because he had acted as a partner in more than one previous successful residence visa application.

In a successful appeal to the IPT, the tribunal found Zhang had special circumstances - arising from the best interest of her son and unborn child, her genuine and stable partnership with her NZ-citizen husband, lack of other pathways to residence and the family unit's difficulty to relocate to China - to warrant a ministerial consideration.

The tribunal accepted it was not feasible for the family unit to relocate to China, where the son and husband are not citizens.

"If the decision was made that the son accompanied her, this would result in separation from his father. He would also be leaving his country of citizenship and relocating to a country he has no familiarity with," the IPT decision said.

"The Tribunal finds that it is in the best interests of the son that the appellant remain living in New Zealand permanently, where she is able to provide him with the necessary care needed.

"Further it finds it will be in the best interests of the unborn child, upon his birth, that he also remains in New Zealand, with both his parents."

The IPT said it was satisfied to the "genuineness and stability" of their relationship and that Chen's previous relationships were also genuine and had broken down for legitimate reasons and not as devices for immigration.

Zhang said she has had sleepless nights since receiving the minister's decision and was worried for her pregnancy and the status of her unborn child, due in August.

Chen said he felt a "totally let down and discriminated" against by the minister.

"I feel the outcome would have been totally different if my wife was wearing a headscarf," he said, in reference to visas being granted to the mosque shooting victims and their families.

INZ Manager Michael Carley said there was no right of appeal after a request made to the minister is declined.

Temporary visas have been approved for all victims and their families in line with their current status in NZ.

"The Government is currently considering residence options for those affected by the shootings and will make an announcement in due course," Carley said.