The ministry told Dr Greg White it was suspending his authorisation to claim for maternity service fees as part of a new vaccine mandate applying to health workers and that he risked committing an infringement if he continued to claim such fees.
The ministry has since apologised and it confirmed a similar mistake had affected at least one other person.
Dr White received his booster shot in November last year.
He would have been happy to provide verification, if only the ministry had asked him for it before its "vaguely threatening" correspondence with him.
Amendments to a vaccine mandate for health and disability workers came into force on Thursday last week.
It meant Dr White, from the Cromwell Family Practice, needed a booster shot or a medical exemption.
Dr White said he received the warning the next day, at the end of a busy week.
"We don’t need bureaucratic nonsense like this. It was so ridiculous, I found it amusing."
A spokesman for the ministry said it had been working through a process of ensuring health professionals working in higher-risk situations met requirements to prevent inadvertent spread of Covid-19.
"In this instance the ministry believes the letter was sent as a result of human error.
"The ministry accepts that Dr White has received his booster vaccine and apologises for what happened," the spokesman said.
Dr White said health professionals were trying to get on with their job.
"We’ve got a lot in front of us in the next few weeks."