Countdown managing director Dave Chambers said the company was exceptionally disappointed the site had to be vacated yesterday.
"Despite a long negotiation and our strong desire to continue to provide the people of Paihia with their only full-service supermarket, we've been asked to stop trading immediately," Mr Chambers said.
Last month the company opened a smaller Countdown in central Paihia which stocked essential produce, though it isn't able to sell alcohol.
Everyone who worked at the Puketona Rd location would been given the opportunity to transition to new positions in Countdown's central Paihia, Kerikeri and Kaikohe supermarkets.
Countdown has occupied the Puketona Rd site for the last 13 years and local residents have said they are upset at its closure.
One woman, who did not want to be identified, said she had shopped at the store almost every day since it opened and thought the workers would be "devastated".
Locals knew there were some issues but thought they were talking them through, she said.