The Centre, Cove Rd, is closed between Nova Scotia Dr and St Marys Rd.
Waipu Pharmacy, next door to Waipu Cafe and Deli, reported it sustained "extensive damage" because of the fire.
"Thankfully nobody has been hurt. Waipu Deli-Cafe and Harkers Herbal have also lost their businesses.
"We will work hard to get services back up and running ASAP, and will keep the community posted via Facebook as to how you can receive services," the business posted to Facebook.
Pharmacist Brenda Wells said the community would feel the temporary loss of the pharmacy as it was an essential service to the rural community.
She told Newstalk ZB she heard the news at 3am when a staff member called her to tell her the building was burning down.
The damage to the store was significant and she did not expect anything in the building to be salvageable.
"Very devastated. My initial concerns is getting the pharmacy services for the community back up and running, that's what I'll be focusing on, we will need to find a temporary premises.
"Get it set up so people can get their medicines back as soon as possible."
She was in Christchurch for the weekend and is flying back to the North Island today.
The next closest pharmacy in Ruakaka would fill in for her pharmacy until it was back on its feet, she said.
She had been operating the pharmacy for the past six years.
Waipu Hammer Hardware posted to Facebook that three businesses, Harker Herbals, Waipu Cafe and Deli and Waipu Pharmacy, had been "burned to the ground".
Well shocking news early this morning. Waipu Pharmacy has sustained extensive damage in a major fire. Thankfully nobody...
Posted by Waipu Pharmacy on Saturday, 29 September 2018
Northpower, the electricity provider for Northland, is reporting 297 customers in Waipu are affected by an outage.
There have been no injuries reported, the Fire and Emergency New Zealand spokesman said.
It was not yet clear when the town centre would reopen.
