The sub-station compound went up in flames and the fire tenders had a tough time dousing the flames, police said.
The farmers are demanding higher prices for land acquired for the Trans Ganga City Project - a residential project that the UP State Industrial Development Corporation (UPSIDC) is developing.
District Magistrate Devendra Kumar Pandey and Superintendent of Police Madhav Prasad Verma rushed to the spot to pacify the agitated farmers.
Clashes between farmers and the police had started on Saturday in which seven policemen, including an additional SP and deputy SP, were wounded in stone pelting.
The police resorted to lathi-charge and lobbed teargas shells to control the crowd.
The UP State Industrial Development Corporation has lodged an FIR against eight named persons and 200 unidentified people for attacking them at the site.
According to reports, the land in question had been acquired in 2012 but protests by farmers stalled the projects for the following years.
A team of UPSIDC employees tried to start work on the project on Saturday and the farmers turned violent. The farmers pelted stones at the JCB machines and UPSIDC chief engineer Sandeep Chauhan was targeted.
District officials said that the farmers had been adequately compensated and were being "misled by vested interests".
A BJP spokesman, meanwhile, said that more than 1,925 farmers had accepted the compensation and only about 114 farmers were creating trouble.
( With inputs from IANS )