The incident comes four days after the Puri-Haridwar Utkal Express derailed in Muzaffarnagar, killing around 23 people and injuring 72.
"10 bogies of the train derailed of which one overturned, leading to injuries to 100 passengers of which four with serious injuries were rushed to Saifai and Etawah hospitals," said Superintendent of Police, Auraiya, Sanjay Tyagi.
There have been no casualties so far.
Secretary, Home, Bhagwan Swarup said the accident took place due to a loader carrying material for work on dedicated freight corridor. "The accident took place because of a loader carrying sand for track working for dedicated freight corridor. It overturned and came on the track," he said.
"It was not an unmanned crossing. But there was a road parallel to the track on which the loader overturned," Mr Swarup added.
Mr Prabhu made the statement hours after Railway Board chairman AK Mittal resigned owning moral responsibility. Ashwini Lohani, the chairman of national carrier Air India, will replace him as the new chief of the board.
The number of deaths due to train accidents has already reached around 200 this year, the highest in a decade. There have been 62 incidents this year alone.
(With PTI inputs)