More than 60 firefighters have battled a large blaze that ripped through a West Melbourne market on Wednesday night and scorched stocks of fresh produce.

Traders will be left counting the cost after the fire broke out at the Melbourne Fruit, Vegetable and Flower Market, shortly after 8pm.

Twelve fire trucks rushed to the Footscray Road market to find thick clouds of smoke coming from the first level of a two-storey facility.

Crews worked quickly to set up hose-lines and send firefighters with breathing apparatus into the burning building.

Metropolitan Fire Brigade incident controller Frank Stockton said the fire was based in a cool room on the ground floor, before spreading throughout the building.

"We had very serious concerns when we saw the amount of smoke coming out of the first floor," he said.

Mr Stockton could not estimate the damage to the crates of fresh produce or the facility, but said the fire damage was substantial.

"Crews are checking whether it has gone any further through the first floor boards," he said on Wednesday night.

One of the market’s managers said he feared the damage was to wholesale fruit, vegetable and flower stock.

A fire brigade spokeswoman said the fire had been "extremely large", and the cause was not yet known.