A police officer has undergone surgery for severe facial injuries after the front windscreen of the van he was driving was speared by a pole in a collision in Melbourne's CBD.

The marked van struck the rail separating pedestrians from tram platforms between Flinders Street Station and Federation Square about 2:15am on Tuesday.

The 33-year-old officer had earlier been in a critical condition, but is now stable.

Police said the van had its lights on and was travelling along the tram tracks at the designated speed limit when it struck a pole.

The pole speared the front windscreen and continued through the cabin before going through the rear of the vehicle.

Police Commander Dean Stevenson said the officers in the van were on their way to help paramedics with a difficult patient when the crash happened.

"Given the weather and the angle they were coming at, [the pole] would be hard to see," he said.

"There's nothing to indicate there has been a loss of control.

"[It's] not unusual for emergency services to be on the tram tracks, but I don't know what lead to the decision to use that part of the tram tracks."

Police Commander Stevenson said it was a close call for the young officer, who has been with the force for three years and has a young family.

"He's got serious head injuries. The railing struck him in the left side of the face," he said.

The officer was taken to the Alfred Hospital, while a second officer in the passenger seat sustained minor injuries.

Conditions were wet overnight on the road, with the CBD receiving five millimetres of rain.

A Yarra Trams spokesman said the scene has been cleared and trams are running on Swanston Street as normal.

Police said the Major Collision Investigation Unit detectives were at the scene and the investigation is ongoing.