He said they diverted a senior staff member from another clinic to the affected team, closing the other clinic at Airport Oaks earlier than usual.
A woman who was booked for a booster shot at the Airport Oaks clinic that afternoon told the Herald she was turned away.
"I turned up to find a message on the front door saying it was closed for the day," she said. "When I asked the nurse walking out why, she said boosters had been stolen."
Fredericson said the clinic was already "flat out" with the whole industry facing a staff shortage and was now preparing for the next wave of the outbreak.
The incident comes as New Zealand is in the midst of a campaign to boost the eligible population with a third dose of the Covid-19 vaccine.
There has also been a steep rise in Covid cases signalling the start of widespread infection, after a slow start to the Omicron outbreak in January.
GPs are bracing for a battle with the virus, with Royal New Zealand College of General Practitioners president Dr Samantha Murton saying the industry is feeling under pressure.
Reports of frontline health care workers facing abuse have grown since the start of the pandemic. Retail staff are also being threatened on a daily basis by aggressive customers who refuse to wear masks in line with public health measures, according to industry body Retail NZ.
Thousands continue to protest against Covid-19 health measures and the vaccine mandates on Parliament grounds, disrupting traffic, business and life in the capital Wellington.