New arrivals into the country are now being put into managed isolation in hotels outside Auckland because the city's quarantine sites are full.

Today's two new Covid-19 cases proves the Government's isolation and quarantine system is working, the heads of the operation say.

Senior Cabinet Minister Megan Woods and Air Commodore Darryn Webb, the pair in charge of the Government's isolation and quarantining operations, spoke to reporters this afternoon.

Woods said today's two new cases were picked up as part of the new testing regime in managed isolation.

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New quarantine facilities outside Auckland would be required, she said.

"Covid is growing, not slowing," Woods said in reference to the global pandemic.

Webb said Auckland's quarantine facilities were now full. Three planeloads of travellers from Australia were yesterday taken by buses to Rotorua.

Angry travellers says they arrived in New Zealand yesterday and were put on buses to Rotorua with no warning.

Webb conceded that communication to those travellers could have been better.

A total of 4272 people were now in managed isolation and with more flights expected this week so the Government was now approaching capacity in Auckland.

Repatriation needed to happened in a safe and managed way so there would be some inconvenience to passengers, Webb said.

"I make no apologies for the tough rules that are in place."

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He estimated that 98 per cent of people returning to New Zealand were Kiwis coming home.

The police presence at hotels had also been increased.

Webb said 232 people were now in Rotorua across two hotels, the Ibis and the Sudima.

The Rotorua hotels had good capacity to take the number of people arriving back. They have been working with them for sometime already so this was just brought forward.

Use of the Stamford Hotel in Auckland was on hold while he reviewed the arrangements there. An air bridge connecting two parts of the building was likely to have to be blocked, and he wanted to review a shared fire exit used by hotel guests and apartment residents in the same building.

Woods said a review due this week would look at all facilities and how they stand up.

"We need to make sure we have the confidence in those facilities so we can stop Covid getting into our communities. What we have seen this weekend with the positive tests is that the system is working," she said.

When asked if there has been a major lack of planning, Woods said it speaks to the complexity of planning that was already in place.

"This didn't need to be done quickly, the work had already been done and they were going to be brought on next this week."

Webb said 60 Auckland hotels were scoped but only 18 hotels across Auckland and Christchurch were being used until the two Rotorua hotels were brought into use because of strict requirements.

When asked why people still weren't being tested on days 3 and 12 of managed isolation, Webb said no one would be released for any managed isolation or quarantine facility until there was a negative test.

"Everyone responded in disbelief, they thought it was some kind of joke. But it became clear once we really were out of the city limits that we were on our way to Rotorua," one traveller, who did not want to be named, told the Herald.

Webb confirmed the developments in a statement this afternoon.

"In total, 232 returnees were transferred by seven dedicated buses from Auckland International Airport following their arrival on three flights from Australia yesterday," he said in the statement.

"I acknowledge that those arriving on this flight had an expectation they were completing their managed isolation in Auckland. However, an increase in arrivals returning to New Zealand has required alternative plans to be put in place.

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He said there had been a plan to use the Stamford Hotel in Auckland as an isolation facility – but that plan was "on hold until I am satisfied it is a suitable as a managed isolation facility".

National's health spokesman, Michael Woodhouse, said the residents of Stamford Plaza deserved better from the Government and the whole process was a shambles.

"The Government's lack of a clear plan for the use of the hotel as a managed isolation facility and complete lack of communication highlights what a disaster this whole process is."