Mr Kannanthanam's name as the party candidate for the bypoll to an Upper House seat from the BJP-ruled Rajasthan was announced by its chief Amit Shah, a party statement said.
The Rajya Sabha seat was vacated by former Union minister M Venkaiah Naidu when he became the Vice President. The notification for the bypoll will be issued on October 30 and the last date for filing nominations will be November 6.
The 64-year-old bureaucrat-turned-politician, who was appointed as the Minister of State for Tourism (Independent charge) in September, is expected to get elected as out of a total 200 members in the Legislative Assembly, the BJP has 160 MLAs followed by the Congress that has 24.
Mr Kannanthanam, a Kerala cadre IAS officer, first came into limelight during his tenure with the Delhi Development Authority in the 1990s and earned the sobriquet 'demolition man' after he got scores of illegal constructions razed.
He served as the district collector of Kottayam in 1988 and helped make it the first 100 per cent literate town in India the following year.
Mr Kananthanam, who is also the Minister of State for Electronics and Information Technology, started his political journey when he was elected as an independent MLA backed by the CPI(M) in Kerala in 2006. He resigned from the civil services earlier that year.
He joined the BJP in 2011 and is a member of the BJP National Executive.