In his resignation letter sent to TDP chief N. Chandrababu Naidu, Khan said the alliance with the BJP amounts to strengthening the communal forces.
Khan, who is also editor of Urdu daily 'Siasat' said he had joined TDP as he believed it was a secular party but now that it has joined hands with a communal party, he can't remain in the party.
He said it was unfortunate that Naidu changed the party's policy on secularism and backed BJP's prime ministerial candidate Narendra Modi, despite the fact that the latter presided over 2002 riots in Gujarat.
Last month, Khan had decided not to contest the polls. He was TDP candidate for Lok Sabha from Hyderabad in 2009 but was defeated by Majlis-e-Ittehadul Muslimeen (MIM) chief Asaduddin Owaisi.
The TDP's move led to resentment in the party leaders in both the Telangana and Seemandhra regions. The TDP leaders are unhappy with the leadership for allotting the BJP certain parliamentary and assembly seats considered the TDP strongholds.
TDP's legislator from Medak M. Hanumantha Rao resigned from the party. He was unhappy with the party's move to leave Malkajgiri Lok Sabha seat for the BJP. He decided to contest for the parliamentary seat as an independent.
Senior TDP leader Kodela Sivaprasada Rao is also angry with the party leadership for leaving Ongole Lok Sabha seat for the BJP.
Under the seat sharing agreement, the TDP has left 47 assembly and seven Lok Sabha seats in Telangana and 15 assembly and five Lok Sabha seats in Seemandhra for the BJP.