Police said some men pelted stones damaging vehicles parked in the office complex. A case has been registered and investigation was underway, they said.
The early morning attack capped a spate of similar attacks on rival party workers' houses in parts of the district following skirmishes between cadres of CPIM and BJP in the past couple of days.
Alleging collapse of law and order in the state, BJP claimed the attack was an attempt on the life of its state President Kumanam Rajasekharan, who was present in the office at Kunnukuzhi locality at that time.
The party alleged that activists of DYFI and SFI were involved in the attack.
The CPI-M hit back, alleging the BJP had planned the incidents to divert attention from the corruption charges over MCI approval against some of its party leaders.
Hours after the BJP office incident, the house of CPI-M state Secretary Kodiyeri Balakrishnan's son Bineesh Kodiyeri came under similar attack, but BJP denied any role in it.
Two police personnel who were on duty at the BJP office at the time of the incident have been suspended, officials said.
This is the second attack on the BJP state office since September last year when a bomb was hurled at it.
Tension has been prevailing in some parts of the district since last night in the wake of the stone-pelting attacks on houses of both BJP-RSS and CPI-M workers, prompting strengthening of patrolling.
Police said additional personnel had been deployed in various parts of the district.
Mr Rajasekharan alleged that the law and order situation in the state had collapsed.
Chief Minister Pinarayi Vijayan should explain and order a probe into "conspiracy of police officials in the attack," he said.
Condemning the vandalisation of BJP office, party state General Secretary M T Ramesh termed it as a "planned conspiracy" and alleged it would not have happened without the knowledge of CPI(M) state leadership.
The attack on party office was "a calculated attempt on the life of Rajasekharan," he told reporters. The CCTV visuals of the incident had clearly identified the attackers as DYFI and SFI leaders, he claimed.
He also alleged that the assailants had police protection and one of the police personnel on duty had opened the office gate.
"Only one policeman tried to stop, but he was also pushed around," Mr Ramesh said showing the CCTV visuals to reporters. Mr Ramesh also said BJP had no role in the attack on the house of Kodiyeri's son. "Let the police probe it," he said adding CPI-M was clever in spreading "false propaganda".