Auckland Council is investigating how a sewage leak occurred at a food court in central Auckland, creating a nauseating stench.

A substance oozing across the floor of the Atrium on Elliot food court eventually emptied out the dining spot on Sunday afternoon while contractors were called in to clean up the mess.

Auckland Council's Food Safety & Health Enforcement leader Alan Ahmu confirmed Council was aware of the incident and an investigation was underway.

"We understand sewage leaked out into the food court seating area on Sunday afternoon," he said.

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Ahmu said Council responded immediately after becoming aware of the incident.

"We are working with the operators of Atrium on Elliot to ensure they have followed the correct procedures and the area is cleaned and sanitised appropriately.

"The safety of the public is of paramount importance to us, and we need to be assured that there is no risk to anyone following this incident."

Speaking to Fairfax on Sunday a witness described the smell as "truly horrid".

Some food outlets kept trading for at least 30 minutes after the noxious ooze seeped through the hall, he said, with only a wall separating the workers from the mess.

"Staff inside looked pained, blocking their mouths as they carried on."

A spokesperson from Drain Ninjas confirmed a crew was in attendance.