"Fifteen passengers and the driver of the train were slightly injured," said Ferrovie dello Stato, the State Railways agency, in a statement at 9pm, after early reports said around ten people had been hurt.
Initial investigations suggested that the incident was caused by human error, after one of the drivers failed to respect a red light, the statement said. The train was travelling at low speed, meaning none of the injuries were serious.
The crash took place in Galugnano station in San Donato di Lecce, a small town of around 5,800 inhabitants in central Salento.
Around 80 people had been on the train, and the passengers were taken to their destinations by bus.
That had been the country's deadliest train crash since a 2009 derailment and subsequent explosion on a train carrying liquid petroleum gas near Viareggio.
In January this year, the former head of Italy's railways and several other executives were convicted over the Viareggio disaster. However, it is likely they won't serve any of it before at least the first of two possible appeals have been heard - a process which could take years.