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Fire and Emergency New Zealand (Fenz) was alerted to the blaze at South Port Bluff, around 11.30pm.
Shift manager Andrew Norris said the warehouse, which was around 7,000 square metres, was engulfed in fire upon their arrival.
"At the peak of the fire we had six fire engines and around 30 firefighters battling the blaze," he said.
The firefighters had the blaze under control by dawn.
There were no injuries reported as a result of the fire.
The warehouse contained palm kernel - a type of stock that Norris said could heat up when stored in large quantities.
The fire was not being treated as suspicious, he said.
A Fenz spokesman said the fire was "going very well when we first arrived".
Firefighters at the scene advised at 1.47am today that the fire was under control, but some firefighting continued beyond this, he said.
Fenz Invercargill Station Officer Jodi McHugh said that Bluff volunteer firefighters had twice
attended the building this morning, at 7.45am and about 11.30am, to deal with "minor hot spots''.
She understood that a loader had earlier been "on fire within the building'' and that some wall-linings at the complex had been damaged.
She believed the building had survived structurally, but that would be a matter for engineers to investigate and determine, she said in an interview.
Meanwhile, Fiona Mathiassen who took the picture said firefighters were "lucky" it was not worse.
South Port general manager Geoff Finnerty said the fire took place in a warehouse leased by a third party.
The port was working with authorities and an investigation into the blaze was under way, he said.
ODT and NZME