Immigration New Zealand (INZ) is considering whether to allow refunds for those who have applied for residency.
An immigration lawyer says the refund process for 50,000 binned visa applications announced on Wednesday is a "disaster" waiting to happen.
The government will cancel and refund visitor, student and work visas of applicants who are offshore.
Many people - including tour groups, students and workers - have not been able to enter the country because of the pandemic.
But some still want their visa to be processed and be kept in the system for when the border reopens.
There are concerns over how long the refunds will take.
"I think it's going to be a disaster," immigration lawyer Elly Fleming said.
"Just judging from the way the last automatic visa extensions have been handled - we've had clients waiting for six months for those to be processed in the system - I can't imagine how they will handle such a large refund of fees."
While visa fees and levies would be refunded, that did not assist applicants who had paid for immigration advice or other expenses they had incurred, she said.
INZ acknowledged in a statement there would be delays.
Border and visa operations general manager Nicola Hogg said processing the refunds "is a significant administrative exercise for INZ and is expected to take several months".
"INZ currently has up to 50,000 temporary visa applications on hand from individuals who are offshore that we are unable to process. These are mainly visitor, student and work visa applications. Many of these applications have been sitting in the system unable to be processed for around 12 months."
INZ, which has suspended visa processing for offshore applications until February 2022, said it was a fair and pragmatic decision, particularly given uncertainty over border restrictions.
Fees and levies are $246 for visitors, $330 for students and between $270 and $495 for workers, with an estimated refund bill of $14 million.
"INZ is committed to ensuring everyone gets their money back and will contact all individuals who are to receive a refund at the time their refund is being processed," Hogg added.
"People can then use the refunds to apply for a visa in the future as borders start to reopen."
Other concerns centre on INZ comments that it was also "reviewing the approach to refund requests from other visa groups, including some residence applicants."
There are 30,000 people in queue for residence visas and another 20,000 waiting for their expressions of interest for residence to be looked at.
INZ said no decisions had been made.
The agency is already processing refunds for residence visa applicants who were unwittingly placed in a non-priority queue for skilled migrants, which has led to waits of two years.