Hawke's Bay itself was exposed to Covid-19 by infected passengers aboard the Ruby Princess cruise ship, the last to dock on March 14 before the door swung shut on cruise visitors.
Once in Napier the virus spread to rest home residents at Gladys Mary Care Home and several health workers, before the cluster that infected 16 local residents was eventually stamped out.
Government restrictions preventing cruise visits remain, and are not expected to lift this season.
Hawke's Bay Tourism said the financial loss for the season ahead was equal to the spending of 250,000 tourists brought into the region through the sea.
For the 2019/20 season, despite an unanticipated end on March 15, cruise ship spending in Hawke's Bay region totalled more than $27 million, Statistics New Zealand said.
For Jeffares, the decision to close down the gift shop on Emerson St did not come about lightly, but regional tourism could not make up for the loss of trade, he said.
Napier Mayor Kirsten Wise said she was confident Napier was doing "all we can as a city and as a region to maintain and grow our domestic tourism market to get us through post-pandemic tough times".
"We have many top events to look forward to as well, including summer F.A.W.C. and the Art Deco Festival."
Council facilities were doing well, she said.
The National Aquarium of New Zealand, the mini-golf centre, Bay Skate and the Faraday Centre have seen an increase in visitor numbers compared to last year.
Right after lockdown, Hawke's Bay Tourism launched its Baycation campaign to support domestic tourism. It's seen an immediate impact - visitor spending increased by more than any other region in August - up to $45 million.
Hawke's Bay Tourism chief executive Hamish Saxton said building on the success of this initial campaign is essential to "maintain momentum".
"Investment is being made to promote the region to encourage visitation over the spring, summer, and autumn periods."
Napier City Business spokeswoman Pip Thompson said most shops that had closed down since the pandemic began in Napier and Hastings were not necessarily shutting because of Covid-19.
"The majority of businesses in Napier do not rely on cruise ship economy. We have been fortunate, Hawke's Bay has been a destination where people have been able to come to and enjoy so ultimately the pandemic has not had an impact on Napier city."