A major incident was declared when two EMR services to London St Pancras collided at 17:15 BST, just south of Elstow, near the road interchange of the A421 and A6.
Eleven people were very seriously injured, a further 32 were described as injured and 57 had minor injuries, East of England Ambulance Service confirmed.
Police said 28 people remained in hospital, including nine in a critical condition.
The two trains involved were the 16:40 from Corby in Northamptonshire and the 15:50 service from Nottingham.
The Rail Accident Investigation Branch, which is working with British Transport Police to establish the circumstances of the crash, expects to provide an update in the coming days.
Trains have been disrupted since the incident, with EMR suspending services to and from London St Pancras over the weekend.
Thameslink has urged passengers to travel only if necessary.
Network Rail said the line between Bedford and Luton was expected to remain closed until 28 June while repair work and investigations continued.
Brett Byatt, who had been travelling to St Pancras from Bedford when the crash occurred, said other passengers “went flying into one another” after the collision.
He told BBC Breakfast he heard a “boom” followed by “shrieks and groans of pain” after the collision.
