Plumes of thick black smoke has been visible across the city as fire crews from across West Yorkshire fight the blaze, at a single storey building on the Junction 41 industrial estate, just off the M1 between Leeds and Wakefield.
The fire service said the fire is at Rathbones Kear Ltd, a bakery operated by Morrisons on the estate in Stephenson Way.
There are no reports of anyone being injured and West Yorkshire Police said they do not believe that the fire was caused deliberately.
Inspector Paul Maxfield, of Wakefield District Neighbourhood Patrol, said: “Due to the size of the fire, a large number of fire appliances were deployed which necessitated road closures around the scene. The fire is not being treated as suspicious and there were no serious injuries but a small number of members of staff were treated for smoke inhalation.
“We are continuing to liaise closely with the fire service to assist with their management of the incident and are doing everything we can to minimise disruption to neighbouring businesses and the surrounding community.”
Police have closed Kenmore Road, Wakefield, in both directions to free up access for emergency crews and have reported significant congestion around the A650 in Wakefield.
Officers are advising people to avoid the area.
One Twitter user reported small fragments of debris landing in their garden some two miles away.
A spokeswoman for West Yorkshire Fire and Rescue Service said the alarm was raised at 4.15pm and that at the height of the incident there were 15 fire appliances in use to bring the fire under control.
She said that 80 per cent of the building was on fire, encompassing an area of 100 metres by 80 metres.
Morrisons has a distribution depot at the Junction 41 estate, which is home to dozens of businesses.
The supermarket chain, which has headquarters in Bradford, did not wish to comment on incident at this early stage.