Two engines would remain at the scene until about 6pm as a precautionary measure.
"There's been nothing to say it was suspicious.''
Countdown spokeswoman Kate Porter said everyone was evacuated without injury. ``All our team and customers were fine.
"The store is currently closed while we assess damage. We're not allowed in at the moment.''
Donna Davenport from the adjacent Car Park Cafe said she could see smoke billowing out of the building.
"It looks like it might have died down now, but there was flames billowing out everywhere.''
The fire did not appear to have spread to neighbouring buildings and the supermarket had been evacuated, Ms Davenport said.
It was the second time the building had caught fire. In June 2009, a blaze seriously damaged the supermarket when it was branded as Woolworths.
Waiheke Art and Craft Supplies owner Gaye Hartley said today's fire wasn't as big as the last one.
Customers and the entire staff from Countdown and neighbouring Placemakers were evacuated to the carpark, she said.
"The whole main street was blocked off, ... [there were] cars and people everywhere.''
The smoke seemed to be coming from the same area as last time, near where a cardboard compactor was based, Ms Hartley said.
The Fire Service didn't take long to get the blaze under control, she said. "They're still there now but the damage is already done.''
The owner of the building was organising for generators to be shipped over from Auckland so the neighbouring businesses could continue to run, Ms Hartley said.