New World stores could either be completely out of stock or have quantity measures in place, spokeswoman Antoinette Laird said.
"We're working closely with vendors to secure as much stock as possible, and exploring sourcing new brands to fill the gap, but volumes are limited due to international demand," she said.
"We're also seeing significant demand and out of stocks for other antibacterial products such as hand wash, antiseptic liquid, face masks, bleach and/or antibacterial wipes.
"If a customer's local store is sold out of the antibacterial products they are looking for, we ask for patience as we secure more stock and get it on store shelves."
Customers could also visit the Ministry of Health website for information and recommendations on how to be prepared and take care of themselves and their families, Laird said.
Elsewhere, Countdown stores had also limited the number of hand sanitisers customers could buy - also a maximum of two.
The limitation had been put in place for about a week because of increased demand, a spokesperson for the supermarket chain said.
"Similar to Foodstuffs, we're working with our suppliers to manage this as best we can," the spokesperson said.
The total number of virus carriers has now hit 454, according to Japan's public broadcaster NHK news - nearly 13 per cent of the 3600 people who were on board.
Among the passengers are 11 New Zealanders who are expected to be evacuated by Australia shortly.
Li was mourned around the world after the ophthalmologist sounded the alarm about the spread of the virus, before being detained by the Chinese government.