Prime Minister Jacinda Ardern has spoken of needing to avoid a "double tragedy" if a traveller were to spread the virus.
The Ministry of Health said the border rules could be "very distressing" but it was taking a precautionary approach.
Among those turned down for a dispensation from managed isolation were two sisters from Melbourne who spoke to RNZ last week about travelling to be with their dying mother.
Officials have been looking at the controls as the country moves toward level 2 and what could be put in place to manage the risk.
Since border controls were tightened on March 28, 6355 travellers have been required to stay in managed isolation in Auckland hotels and quarantine facilities, paid for by the Government.
Of the total, 296 have applied for an exemption from having their isolation managed this way, and 29 have been granted.
Exemptions granted:
* 16 on medical grounds * 5 medivacs - unwell people going straight to hospital * 1 exceptional circumstances (left managed isolation 16 hours early to get transport) * 2 transit (collecting children and leaving the country) * 2 unaccompanied minors (parent or guardian joining them in managed isolation) * 2 essential worker exemptions * 1 extradition (to isolate in prison rather than a hotel)