Stocks were also running low at Countdown Supermarket in Hastings, despite the fact they received a fresh supply of the product just two days ago.
"We have got 48 jars of the 250g and 12 of the 175g, - that's all," duty manager Tina Cornforth said.
"There's none of the 1.2kg, none of the 500g and none of the 125g."
Supplies of Marmite would normally come in about once a week, and regular shoppers were already making sure they had enough in the cupboard, Ms Cornforth said.
"It's going quickly, one customer came through today with five jars."
A Napier supermarket contacted by Hawke's Bay Today said there had not been any Marmite on their shelves for the past two weeks.
It was a problem too for Dannevirke Four Square with nothing but an empty space where the Marmite used to be.
Sanitarium general manager Pierre van Heerden said the last containers of Marmite were sent out to distribution centres across the country this week.
But he urged consumers not to "freak out".
"We will get Marmite back, we will be producing it in New Zealand, it will be the same product that we've all come to love."
Sanitarium asked customers to remain calm as it worked to relocate its Marmite manufacturing facilities to a safer part of the Christchurch site. It also encouraged people to ration their use of the spread by eating it on toast, rather than untoasted bread to make it last.
"With toast, it's a little bit warmer so it spreads easier and it goes a little bit further," Mr Van Heerden said.
Once current supplies went dry, people would have to wait a while for another fix, with production not expected to resume until midway through the year.