Khan, who is the Urban Development Minister of the state, has also been booked for his "Kutte Ka Baccha" (puppy) remarks, attacking Narrendra Modi during a poll rally.
Sub-Divisional Magistrate (Sadar) Kunal Silku today lodged an FIR against Khan at Masuri Police station after Election Commission of India yesterday ordered FIR against the close aide of SP supremo Mulayam Singh Yadav.
The charges also include Sections 505 (2) (statements creating or promoting enmity, hatred or ill- will between classes) and 188 (Disobedience to order duly promulgated by public servant) of the Indian Penal Code (IPC).
Police also said that he has also been booked under Section 125 of the Representation of the People ACT.
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Before registering the FIR, Ghaziabad DM and ADM held a meeting with SSP to discuss the next course of action on this matter.
In this meeting, the decision to book Azam Khan was taken and within few minutes Khan was registered for his alleged inflammatory speech over Kargil War.
On April 7, Khan had during his party rally in Muslim- dominated area Masuri area, said that peaks of Kargil were not conquered by Hindus, but by Muslims.
The Election Commission had on Friday banned him from campaigning in Uttar Pradesh and had asked authorities to initiate criminal proceedings against him.
Speaking in Rampur on Friday, Azam Khan said he did not speak anything wrong and was a "nationalist". He said that the EC's step was "premature" as he was not given a hearing and he will urge the commission to review its decision.