Chief executive Miles Hurrell said it would enable the co-operative to keep growing.
The new cool store will be the size of three rugby fields.
It will be able to house around 26,000 tonnes of cheese, and increase the site's capacity by about 5000 tonnes.
The Whareroa site processes up to 12.5million litres of milk per day and produces 30% of Fonterra's cheese, and several other products including butter, casein and powders.
Construction will begin next month and take three years in two phases.