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Joint Head of MIQ Brigadier Rose King said two positive community cases staying at the Jet Park Managed Quarantine Facility absconded at 4.45pm yesterday and are yet to be located.
"MIQ is working with police to locate them."
It follows an incident yesterday when a community case staying at the Novotel & Ibis MIQ facility in Ellerslie allegedly escaped at about 12.50pm, before being found by police and taken into custody at 1.14pm.
King said this case had no contact with anyone in the community and there was likely to be a low risk to the public.
But she said the fact that people have absconded from two of the country's MIQ facilities was "disappointing and unacceptable" and an investigation had been launched into how these events occurred.
She said the facilities were not prisons and the individuals had "wilfully absconded".
"There are rules in place for every single returnee from overseas and now the positive community cases, and we expect people to follow these during their stay in managed isolation or quarantine. This is so they can return to the community safely, while ensuring the safety of all New Zealanders.
"Deliberate breaches like this can put the wider community at risk."