The New World Metro on Queen Street is now open.
A worker said they closed for about two-and-a-half hours as they worked to clean the store, when a water pipe burst.
The supermarket was opened again at about 4pm.
Earlier, a duty manager told the Herald the store had been evacuated.
She said someone had been called into clean up the mess.
Customers were being turned away at the door, with them being told "we have had an emergency so we have had to close the store".
A video showed the burst water pipe, in the ceiling spilling out onto the supermarket shelves, flooding the floor with a sea of water that looked to be ankle deep.
Watercare media communications advisor Melanie Verran said it appeared the burst pipe was not under the company network.
"We can confirm there are no breakages in our system," she said.
"From the looks of the video it'd be a problem with a private pipe."
Ms Verran said the supermarket would likely be calling in an emergency plumber to deal with the burst pipe.
It's understood a NZDF aircraft and multiple helicopters are involved.