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The drive-through at Christchurch Arena was set up to fast-track vaccinations for customer-facing essential workers but closed on Saturday.
More than 13,000 people got their jab there and received a follow-up booking for their second in three to six weeks' time.
They have now received a message telling them the drive-through has changed its hours of operation and their second appointment is no longer available.
And they have been asked to rebook through the Book My Vaccine website or by phone.
The Canterbury DHB says the drive-through was only temporary to get essential workers vaccinated as quickly as possible.
It says it has more than 100 clinics providing vaccinations throughout Canterbury.
Variance from DHB vaccination plan weekly targets to August 29. DHB production plans have been suspended from August 30 to October 3 due to increased vaccination demand caused by the August 2021 outbreak.