The FIR was lodged by Assistant Returning Officer Sanjay Kumar Singh on Sunday at Nehtaur Police Station, police said on Monday. (Agencies)
Khan has been accused of flaring up communal feelings and trying to divide communities on religious lines by his speech on April 11.
After seeing the video footage, Singh lodged an FIR against Khan and SP candidate Yashvir Singh's representative Rajvardhan Singh under sections IPC 505 (2)(Statements creating or promoting enmity, hatred or ill-will between classes), and 125 (Representation of the People Act) besides others.
Earlier, a case was registered against the senior Samjawadi Party leader in Thana Bhawan police station on Saturday for his remarks at an election rally in Jalalabad area of the district on April 8.
Khan had allegedly attacked BJP's Prime Ministerial candidate Narendra Modi saying, "his hands are coloured with blood of innocent people and you should never let any such person rule the country."
Ghaziabad police had also booked the close aide of SP supremo Mulayam Singh Yadav for his alleged inflammatory speech over Kargil War.
On April 7, Khan had during his party rally in Muslim- dominated Masuri area, said that victory against Pakistan during the 1999 Kargil conflict was made possible because of Muslim soldiers and not by Hindus.
One case was registered against Khan for inciting communal passions through his election speech on April 9 in Sambhal district of UP.
The Election Commission had on April 11 banned Khan from campaigning in Uttar Pradesh and had asked authorities to initiate criminal proceedings against him.
The FIR was lodged by Assistant Returning Officer Sanjay Kumar Singh on Sunday at Nehtaur Police Station, police said on Monday.