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Two of the people had underlying medical conditions.
They were a young girl who died yesterday morning in Wellington Hospital and a 42-year-old man who died on Thursday in Christchurch.
The coroner will investigate whether any medical conditions played a part in the death of Zachary Wilson, 19, from Hamilton, who died at home last Sunday without having been diagnosed with swine flu.
The Ministry said swine flu was more than likely the cause of the three deaths.
Following the announcement of the deaths yesterday, Healthline received 2000 calls, director of Public Health Mark Jacobs said.
"There was a definite spike in calls after the news at 6pm, so I encourage people to persevere and keep holding if they call at a busy time and need to wait." Healthline, 0800 611 116, has registered nurses answering calls 24/7.
New Zealand now had 961 confirmed cases, up from 945 yesterday, Dr Jacobs said.
"Swine flu will be with us for quite some time and is continuing to spread throughout the community, but there is no cause for alarm." Swine flu was a mild illness for most, though it could be severe or fatal for some.
"We know that people with some significant underlying medical conditions are at greater risk, however, it's important to remember that overseas experience has shown that some previously healthy people have also been seriously affected by swine flu," Dr Jacobs said.
People should continue to: - stay home if they are sick; - cover their coughs and sneezes; - frequently, thoroughly wash and dry hands.
Anyone who thinks they have the flu and have other significant medial conditions should call Healthline or their doctor.
People should also seek medical advice if flu symptoms worsen, for example if they are having difficulty breathing, get drowsier or if taking medication such as paracetamol or ibuprofen does not lower a high temperature.
There are 62 probable cases of swine flu in New Zealand.
The number of confirmed cases in each region are: Northland (20), Auckland (202), Waikato (45), Bay of Plenty/Lakes (29), Gisborne (2), Hawkes Bay (84), Taranaki (3), Wanganui/Palmerston North (14), Wellington (292), Nelson/Marlborough (22), Canterbury (234), Otago/Southland (14).
Australia has had more than 5250 confirmed cases and 10 deaths.
Worldwide on Friday there had been 89,921 cases, including 382 deaths.