Both parties have confirmed the matter is still before the courts and next due to be heard in September.
Ziwi managing director Richard Lawrence said the new site, on Awatoto Rd, will not have the same issues.
"The custom-built state-of-the-art processing kitchen is designed to mitigate any odour issues for local residents and businesses," he said.
Work on the new kitchen is expected to start in August, with a completion date in September or October 2021.
Napier mayor Kirsten Wise said she welcomed the company's relocation to Hawke's Bay during the region's "most challenging time".
"We welcome any company that would like to do business and create employment opportunities for Napier," she said.
"Any issue about odour control is the remit of Hawke's Bay Regional Council.
"I understand that the plant will be purpose-built and use modern technologies rather than retrofitting an old plant.
"Ziwi will have to comply with the standards relating to odour and I am confident that HBRC will enforce all the appropriate regulations in this situation."
Napier councillor Richard McGrath said it was good to have more jobs in the Bay, and jobs would also be created by building the factory and ongoing local suppliers.
The company's three Tauranga sites will continue to operate until late 2021, when production from these sites shifts to Napier and the three Tauranga sites will close.
All employees at the Tauranga sites will be offered jobs at the new Napier kitchen.