District Health Boards (DHBs) are being forced to reshuffle rosters to give 120 doctors time off to resit a test after a fault with the online system meant some couldn't finish.
Doctors wanting to specialise as physicians sat the day-long theoretical component on Monday along with their Australian counterparts.
But a fault in the annual test locked some candidates out and now everyone will resit a paper-based test next Friday, the New Zealand president of the Royal Australasian College of Physicians said.
It affected 11 doctors at Christchurch Hospital - nine from the Department of Medicine and two paediatric registrars, said chief of medicine Dr David Smyth.
Although people call them junior doctors, they were more senior that some would think, he said.
"They have a good deal of autonomy - they look after patients under supervision on the wards, but they're left to get on with tasks."
Many of the doctors were rostered on for the resit date - 2 March - which would now have to be shuffled, he said.
"We'll have other registrars - senior doctors will have to cover them.
"We're hoping that it won't affect clinic appointments but of course in theory it could do, these people do clinics as well," Dr Smyth said.
"It requires a lot of shuffling to get by."
But any affected patients would be notified, he said.
It was "certainly a fiasco" but if staff needed extra study leave then the Canterbury DHB would go out of its way to provide it, he said.
Waikato DHB had 12 registrars needing to resit and Counties Manukau would not state how many they had.
The three DHBs said they would work with their staff to make sure they were supported and their shifts were covered.