No one was injured in the incident, police said.
The incident occurred around midnight last night, shortly after BJP state president Kummanam Rajasekharan had left the office for Kozhikode, where preparations are on for the three-day National Executive and Council meeting from September 23 which is being attended by senior party leaders and Prime Minister Narendra Modi, party sources said.
At least four workers were on the top floor of the building, housing the office, when the bomb was hurled.
The incident comes close on the heels of a series of sporadic clashes between CPI(M) and BJP workers in the past few months in northern Kannur district.
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Rajasekharan alleged that CPI(M), the lead partner of the ruling LDF in Kerala, had taken law into its hands and police was a "mere spectator."
"Violence of the CPI(M) is increasing each day. A BJP activist was hacked to death in Kannur recently and CPI(M) is behind it," he told reporters at Kozhikode.
BJP leaders P K Krishnadas and M T Ramesh slammed the CPI(M), saying the bomb attack against the party office should not be seen as an "isolated" incident.
"This is a calculated and well planned attack against the BJP and CPI(M) is behind it," they said. All flex boards in front of the office were also destroyed, Krishnadas said.
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Meanwhile, CPI(M) said the BJP's allegations against it were "baseless" and it had no connection with the incident.
"The incident is highly condemnable. Anti-social elements connected with the incident should be immediately arrested", CPI(M) Thiruvananthapuram district secretary, Anavoor Nagappan, said in a statement.
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Meanwhile, state BJP president Kummanam Rajasekharan said the party would observe tomorrow as 'black day' to protest against the attack.
Alleging that CPI(M) was behind the incident, he said "CPI(M) can not destroy our party with bombs and daggers. We will fight back to protect ourselves, if there is no other way".
Rajasekharan was here to attend a review meeting on the preparations for BJP's national council and national executive meetings scheduled to held from September 23 to 25.