They were protesting the alleged incident of desecration of Guru Granth Sahib in a Gurudwara at Kattaiya Pandra village in Amaria area on UP-Uttarakhand border on September 12.
Some of the protesters entered Majhaula railway station and damaged railway tracks, broke signals and barriers there, police said.
BJP leader Varun Gandhi and SP leader Shivpal Singh Yadav reached the spot to pacify the protesters but they did not pay heed to the leaders, sources said.
Heavy police force has been deployed in the area, and police and district administration officials have reached the spot.
"We have deployed heavy police force in the area and strict action would be taken against those found involved in the ruckus," IG RP Singh said, claiming that some leaders were involved in instigating protesters.