While almost 100,000 people wait for a residence visa, some people have accidentally received two.
Immigration New Zealand (INZ) said it did not know how many duplicates had been issued and apologised to those affected.
It is the latest in a series of glitches in the $56.6 million ADEPT computer system, which was introduced to streamline visa operations.
More than 550 production defects or bugs had been identified by the start of November.
"As with any new large-scale technology and business change programme there is a period of bedding-in required, where staff are learning the new processing model and procedures," said border and visa operations general manager Nicola Hogg.
"During this time, it is also normal to identify and address any issues, however where issues have occurred, we have worked to identify and resolve these as quickly as possible," Hogg said.
"No large-scale technology deployment ever goes without a hitch, and we acknowledge that a number of customers, including immigration professionals have experienced challenges with the new system that has caused frustration and appreciate their continued patience and willingness to work with us to identify and get these resolved."
For most applicants, the system was working well, she said.
"We are aware that some 2021 Resident Visa applicants have been issued a 2021 Resident Visa twice. This is due to a number of reasons, including where an application has had to be reraised in a different INZ system to be processed, and where the addition of secondary applicants after the initial application was received.
"We are currently working through how many people have been impacted by this and don't have exact figures at this stage."
The Association of Migration and Investment said it was regularly raising technical issues with INZ, and work visas were being sent out with no employer name.
Its chair, Nicola Tiffen, said when 2021 residence visas were being issued, there were almost always several extra pages of blank residence visas behind them with no names.
"I worry that people will use these templates to create fraudulent visa documentation, such as for the purposes of gaining employment," she said.
Meanwhile, visitor visa application glitches led to some languishing for months forcing families to cancel flights and Christmas plans with relatives.
Bhupinder Singh Gandhi said it was heartbreaking. His wife's brother had been due to fly tomorrow and he had been unable to find out why he was still waiting for a visa after three months.
"I asked them that, why it's taking so long, and the reply is they are overburdened. But I found that many of my friends' family visas got approved within a week. They applied for the visa a couple of weeks ago. I am stunned that INZ is even unable to let me know the approximate time of processing so we can reschedule or cancel the plans."
INZ incident management team controller Richard Owen said almost 9000 visitor visa applications from August were still unprocessed by the start of November and that stood at 2349 by last week.
"We know we have people depending on us to travel to New Zealand, and we are committed to continuing to improve our services to meet their expectations. We have allocated more people to work through these applications to progress to a decision and if granted a visa, customers will be able to travel soon.
"INZ recognises there is more work to do to process visas at the speed employers, customers and stakeholders expect, and we are focused on continual improvement on our processing rates and customer experience."