Some medical practices still have hundreds of doses of the MMR vaccine while others have completely run out, authorities say.

Stocks of the measles, mumps, rubella vaccine are being moved around the country with a focus on getting them to Auckland clinics where they are desperately needed, as the country awaits a fresh shipment of 52,000 doses.

The Ministry of Health and Pharmac carried out a nationwide stocktake on Monday after numerous reports of shortages. There's been a run on the vaccine amid the worst outbreak of the measles in decades.

Notified cases of the highly contagious disease reached 1149 today across New Zealand, and 959 of those cases are in the Auckland region, according to the Ministry of Health.

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Doctors have warned New Zealand can expect fatalities if the outbreak continues. Vulnerable groups such as young babies are at high risk.

Starship Children's Hospital is currently treating two patients for measles, although their ages have not been revealed. Both were stable, an Auckland DHB spokeswoman said.

The outbreak has even reached inside the city's prisons. Three prisoners are in isolation at Auckland Region Women's Corrections Facility following concerns they have been exposed to measles, while the prison's Mothers with Babies Unit has been placed in quarantine as a precaution.

Health authorities have been urging people to check their vaccination status and that of their children, and to get a dose of the MMR vaccine if they were not up to date or could not find records.

There had been a spike in vaccinations as a result, with 20,000 jabs per month, up on the typical 12,000 per month, the ministry said last week.

Medical centres report being overrun with inquiries about the vaccine - but many have begun turning people away after running out.

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One father who tried to get his measles jab in Birkenhead told the Herald his appointment had been delayed for a week before being cancelled. His booster shot was rescheduled for Monday but was cancelled altogether after the centre said they could not be sure when supplies would arrive.

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He had only had one measles jab as a youngster so was trying to get his booster to ensure his young baby was protected.

A planned pop-in clinic at Albany run by PHO Comprehensive Care was his next port of call.

But that event had also been cancelled because of "unprecedented demand for measles vaccines", according to a post on social media from the PHO.

People would be kept posted on alternative clinics when they were available.

Regrettably, due to unprecedented demand for measles vaccines, the clinic planned for Saturday 14 September at 42 Tawa...

Posted by Comprehensive Care on Monday, 9 September 2019

Shortages have also been reported in Papakura as well as at GPs in Tauranga and Rotorua.

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Supply problems have plagued Auckland in particular.

Associate Health Minister Julie Ann Genter told RNZ today some clinics had hundreds of vaccines while others had none.

"We're focused on ensuring there are vaccines available particularly in priority areas in Auckland to contain the outbreak."

The Ministry of Health said it had worked with DHBs and the distributors on a stocktake of MMR vaccine supplies.

It now had "greater clarity" on supplies. The vaccine would be redistributed with a focus on Auckland, where the three DHBs were working directly with Public Health Organisations and GPs to manage stocks.

For the rest of the country, the ministry and Pharmac were working with the distributors to get vaccines to places that were low on stock or had run out.

More than 54,000 doses of vaccine were distributed last week, the ministry said.

Pharmac has promised fresh supplies of 52,000 shots are due to arrive later this week.

The ministry said it was important to manage the remaining supplies "appropriately" in the meantime.

"The message about vaccination remains the same: all children should get their vaccinations on time to ensure the National Immunisation Schedule remains on track.

"In Auckland, vaccination efforts are targeting those communities most affected, namely Pacific peoples, and children under 4 years of age and aged between 15 and 29 years to get on top of the outbreak."

Figures published on Friday showed that, of the 1111 cases since January 1, 554 were in unvaccinated patients. The vaccination status of another 465 was not known. Another 28 patients had had one shot and 64 were fully vaccinated.