Health officials had contacted all but 18 of the 356 people on Saturday's Air New Zealand flight NZ1 from Los Angeles and were yesterday still trying to track the remainder down.
Otago and Southland medical officer of health Dr Derek Bell said the five had been "on the road, or in the bush" before they contacted health officials.
They had not known about news of a potential swine flu pandemic, he said.
The five went into voluntary quarantine in hotels and were taking the antiviral medication Tamiflu, bringing the total number of people in isolation in Otago and Southland to 27.
Dr Bell would not say where in the region the five were, saying there were people in quarantine "all over Otago and Southland".
None were sick and there was no increased risk to people in the region, he said.
Wakatipu health officials were taking it as a good sign that no passengers asked to be assessed for swine flu during the first assessment of international arrivals at Queenstown Airport yesterday.
Staff were standing by when 68 passengers on Qantas flight QF121 from Sydney arrived in Queenstown at 1.17pm.
Passengers on the A320 Airbus were handed Ministry of Health travel health notices which recommended travellers followed the same precautionary measures as with seasonal flu, and described the symptoms of swine flu.
The notice advised New Zealanders who have recently travelled to Mexico, California or Texas, and who develop flu-like symptoms, to "seek medical attention immediately".
United States Army captain Brent Zewadski and wife Jessica, of Florida, were visiting Queenstown during his two-week leave from service in Afghanistan.
Capt Zewadski said the mood among passengers was calm and normal and that officials were "on top of it".
Mrs Zewadski said: "The man at customs said if I had any symptoms to see the nurses because I'm from the States, but it's Florida and I don't go touching swine."
Nationally, there are 13 confirmed cases of swine flu, including two people outside the original group of Rangitoto College pupils who fell ill.
Another person on the same flight as the pupils, who were returning from flu-stricken Mexico, and a traveller from either the United States or Mexico, who was not on that flight, have tested positive for influenza A.
Around the country there are 96 suspected influenza A cases and 179 people in isolation.
Health Minister Tony Ryall said further cases could be expected.
The Government had made an order-in-council making non-seasonal influenza a notifiable disease.
Nineteen countries, including New Zealand and Australia, now have suspected swine flu cases.
Deputy public health director Fran McGrath said it was too early to say why swine flu was proving so lethal in Mexico, while those infected in New Zealand were showing more mild effects.
"We do know that different types of common infections, like influenza, often do have different patterns in different countries, depending on the state of wellbeing of people and depending on how it is happening in that country," she said.
Screening of international passengers coming into New Zealand is continuing at Auckland Airport and 16 passengers experiencing flu-like symptoms were detected yesterday.
People with concerns about swine flu should phone the national free healthline (0800 611-116) or their medical centre. They should not just turn up at hospitals or medical centres.
- Additional reporting by NZPA
