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The container ship Rio Madeira was off the coast near Karitane yesterday while crew were tested, "out of an abundance of caution", a Southern District Health Board spokeswoman said last night.
The ship was meant to arrive at Port Chalmers at 1.45pm yesterday from Lyttelton.
SDHB medical officer of health Susan Jack today confirmed the "documented old Covid-19 case", and said all other crew had tested negative.
She said he had fully recovered, had no symptoms and was not infectious.
"He poses no risk to other crew members, port workers or the general public."
In his media briefing today, Director-general of Health Ashley Bloomfield referred to the case, saying the person had returned a weak positive result, and because it had been previously reported in India it would not count on New Zealand's tally.
A pilot was sent out yesterday but did not board the Rio Madeira and returned to the port. The ship dropped anchor and remained where it was.
Port Otago chief executive Kevin Winders yesterday said it was not confident that the ship was in a position to be brought in.
Ships had to be declared "Covid-free" before berthing.
"If they have got any suspicions and any concerns they always err on the side of caution," he said.
Port Otago's schedule shows the ship is now scheduled to arrive in Port Chalmers around 3pm today.