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Apples and peaches on sale across the country could have been contaminated with Hepatitis A, the Ministry for Primary Industries says.
The ministry advised consumers to cook suspect fruit thoroughly before eating it or dispose of it.
A worker at a Hawke's Bay packhouse was handling Royal Gala and New Zealand Beauty apples and Golden Queen peaches over a four-day period while infected with the virus.
The ministry said the risk of contracting the illness from the fruit, sold between February 27 and March 13, was "relatively low".
While some potentially affected fruit had been traced and withdrawn from sale, it was likely about 1400 cartons had been sold, ministry deputy director general Scott Gallacher said.
All the fruit was for domestic sale.
Hepatitis A virus can remain infectious on the surface of fruit for months and transmit infection to other handlers and consumers.
Early symptoms are fever, loss of appetite, stomach pains and nausea. Further signs include skin jaundice, yellowing of the whites of eyes, dark urine and pale bowel motions.
Mr Gallacher said anyone with health concerns should contact their doctor.
The warning affects:
*Royal Gala apples from: All Countdown, Fresh Choice and Super Value and supermarkets in the North Island.
*Golden Queen peaches from: All Countdown, Fresh Choice, Super Value and supermarkets in the North Island. Pak'n Save, New World and Four Square supermarkets from to Taupo to Kaitaia
*New Zealand Beauty apples from: All Countdown, Fresh Choice and Super Value supermarkets in the South Island.