The British Transport Police are appealing for help to trace the ownership of the animals, who were straying around the Fen Road level crossing at Milton.
The collisions occurred just before 5.15pm, with the animals struck by locomotives going in both directions.
“We are very keen to find out who the horses belong to,” said Sergeant David Barker, who is investigating the incident.
“At the moment it is not clear how many horses died in the incident. However, we now believe that at least 12 were killed.
“I also want to know how the horses came to be on the tracks.”
The breeds of the horses remained unclear at this stage. He said the animals were thought to have come from fields in the Fen Road area.
Barker said officers were keeping an open mind on the cause of the incident at this stage.
Cambridgeshire Police, the ambulance service and fire service were called to the scene.
A female passenger was taken to hospital with minor injuries and was later discharged.
At least two trains were understood to have been involved, travelling between Birmingham and Stansted Airport. One of the services was known to be carrying 220 people.
One media report suggested the impact of one of the collisions had derailed a carriage, although this could not be confirmed.
Train services in both directions were disrupted while the track was cleared and checked.