I understand the frustration of commuters when there are delays, but this should never be allowed to find expression in violence.

Transport Minister Dullah Omar

Witnesses said passengers "rampaged" through the 100-year-old station attacking employees and security guards and setting furniture on fire.

About 80 firefighters worked through the night to contain the blaze.

Station managers say the roof and third floor of the historic building were destroyed.

Damage to the station is being estimated at about $7m.

Police deployed

Early on Tuesday, about 100 police and army officers were deployed at stations were trains were not operating to prevent disturbances during the morning rush hour.

Some police were deployed on horseback and barbed wire was erected around Pretoria railway station's main car park as thousands of commuters were prevented from making their normal journey to work.

Transport Minister Dullah Omar condemned the vandalism.

"I understand the frustration of commuters when there are delays, but this should never be allowed to find expression in violence. It is most regrettable," he said.

One person was taken to the hospital to be treated for smoke inhalation.

Pretoria Railway Station is used by tens of thousands of commuters every day.

Visiting the burnt out building on Tuesday morning, Pretoria mayor Smangaliso Mkhatshwa said he was "very, very upset"

"Nobody is allowed to take the law into their own hands, whatever the reasons may be," he said.