A migrant worker who had his resident visa application incorrectly assessed is furious Immigration New Zealand's mistake will see him have to leave the country before the end of the year.

Varun Sharma has lived and worked in New Zealand since arriving on a student visa in 2009 where he gained a graduate diploma in business studies.

A restaurant manager at Fox Glacier's Bigfoot Bar and Restaurant, he applied for a residency visa under the Skilled Migrant Category in October 2018, but was declined by Immigration (INZ) in November 2019.

"Your role does not substantially match the description for a restaurant manager as set out in the ANZSCO [Australian and New Zealand Standard Classification of Occupations]," the decision read.

Immigration was not satisfied Sharma was responsible for planning menus, organising events or arranging the purchasing and pricing of goods. It also was not convinced of his food safety knowledge.

These were all criteria listed under the ANZSCO description for restaurant manager.

However, that decision was overturned by the Immigration and Protection Tribunal in May 2020.

The Tribunal found INZ's approach to the evidence it had been given was "selective and unfair" and the application had not been properly assessed.

It did not say the visa should have been approved, but ordered a reassessment that had to be done by a different case officer.

This reassessment however, was declined in October 2020 because the restaurant had not made a profit in the last six months due to the Covid-19 lockdown.

Sharma said had the application been correctly assessed in the first place, his situation could have been very different.

"I'm pretty upset because they made a wrong decision and this is not what I deserve."

The restaurant's owner Hitesh Talreja said Sharma ran the restaurant and looked after the Fox Glacier Inn and Hostel as he was frequently off-site for extended periods of time.

He said Sharma was more than qualified for the role of restaurant manager.

"He was basically running the whole place."

He also said a previous employee received a resident's visa under the same category doing the same job only two years prior.

"I find that really weird because the same position was used ... and [Varun Sharma] was rejected because somebody did not know how to do their job."

Talreja said the reassessment should have been based on the original application, and not the new circumstances created by Covid-19.

"Using that to refuse his residency was the most unfair thing Immigration New Zealand could ever do."

INZ did not address RNZ's specific questions relating to Sharma's situation, but in a statement a spokesperson said all residence applications were quality checked before a final decision was made.

"We must apply the law and regulations consistently to every application, which may have adverse impacts on a small number of individuals. This can seem unjust and bureaucratic at times, but as a regulator INZ legally does not have the flexibility to go outside the instructions as enshrined in law."

"If an applicant's circumstances have changed, such as their employment or the sustainability of their employer, then INZ must assess if this change means the applicant does not meet immigration instructions."

"The Immigration & Protection Tribunal considers appeals and is able to take into account any humanitarian or special circumstances in the individual case that may warrant the grant of a residence visa as an exception to instructions."

Sharma spent about $15,000 on legal fees to have his application correctly assessed, but has now run out of money. He cannot afford to return to the tribunal or seek legal assistance.

His current work visa expires in November.