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The ministry says it is a scam and police are investigating.
Addington resident Joshua said the two smartly dressed men knocked on the door on Saturday morning.
The pair claimed they were from a Ministry of Health outreach programme, aimed at boosting community vaccination rates.
"They even had a sheet of paper just explaining the vaccine process and that for $100 they were offering an outreach where like a car would come or someone and they could vaccinate you after work hours."
Joshua knew something was off.
"I'd just heard a lot on the news about being careful of scams and that vaccines are free and that you won't have to pay for them so I was a bit suspicious."
They had a well-rehearsed line for what the $100 would cover, he said.
"They said it would cover the cost of the call-out fee and the petrol, so they said that was a fee on top of some outreach programme was partially funded so it wasn't fully funded."
Joshua said the two men had a portable eftpos machine - pay now, get the vaccine later.
He was not taken in and wants to warn others.
"People [need] to be aware of this and not take it for its face value because they do look very professional," he said.
"It's a very well thought out scam that they're operating."
RNZ contacted the Ministry of Health about Joshua's experience.
In a statement, the ministry said it was a scam and Covid-19 vaccinations were being offered for free.
"All vaccinations are being led by locally by district health boards (DHBs) and are delivered by healthcare service providers in their communities, such as GPs, pharmacies, Whānau Ora and other legitimate providers," it said.
"Therefore, anyone trying to charge for vaccinations, or arriving unannounced and going door-to-door claiming to be from the Ministry of Health and offering vaccinations is not legitimate."
Home vaccinations may be offered by DHBs for those unable to make it to a clinic, but this would only be arranged by their healthcare provider, the ministry said.
Police say they have received reports of two people going door-to-door in Christchurch offering vaccinations for a fee.
In a statement police said they were making enquiries and anyone approached should immediately report it via 105.