The police arrested BUP leader Mahendra Dixit on Wednesday morning, used force to disperse his supporters and allegedly roughed up women. The rampaging mob, in turn, took over the station after overpowering the police.
Sensing trouble, the authorities stopped the Mahananda Express at Hathras junction.
The mob set the train ablaze after the passengers got down.
District Magistrate Pragyan Ram Mishra, Superintendent of Police Shiyaram Aditya and three policemen were among those injured in the clashes.
The police first lobbed tear gas shells and then fired in the air. Officials said they had no information on the number of civilian casualties.