The day also saw the Congress-led UDF take out a march to the state Assembly over the same issue.
The BJP and the UDF marched separately, demanding the LDF government's intervention to end the agitation by their respective leaders for withdrawal of the prohibitory orders around Sabarimala.
The BJP workers threw stones and hurled chairs at police personnel outside the state secretariat when the latter stopped them from proceeding further.
The party had announced the march as part of its intensifying protests over the Sabarimala issue.
The protesters raised slogans demanding the government's intervention to end the eight-day-old indefinite fast of BJP general secretary AN Radhakrishnan.
Subsequently, police used water cannon and tear gas to disperse the protesters.
Protesting against the police action, BJP workers, led by general secretary Shobha Surendran and Thiruvananthapuram district president S Suresh, squatted on the road and raised slogans.
Radhakrishnan has been on an indefinite fast in front of the secretariat building since 3 December, demanding the withdrawal of prohibitory orders and various cases registered against party general secretary K Surendran over the Sabarimala protests.
BJP workers, who took out marches at Kottayam, Kochi and Kozhikode, were also stopped by police.
Union Minister Alphons Kannanthanam visited Radhakrishnan at the agitation venue in the state capital.
Kannanthanam later told reporters that the state government should withdraw the ban orders imposed at Sabarimala and all the "false" cases against the BJP workers over the protests at the hill shrine.
The CPI-M-led LDF government must understand the sentiments of the people and take the initiative to end the "hunger strike" of Radhakrishnan, he said.
"Why should Section 144 be imposed in Sabarimala. It is stated that devotees are chanting "nama japam" (Chanting of Ayyappa mantras). Is it a criminal activity?" Kannanthanam asked.
By using tear gas shells and force, government was trying to suppress the protests against the restrictions and prohibitory orders, he said, adding that it was "undemocratic".
The opposition UDF took out the march demanding that the government intervene and end the indefinite 'satyagraha' by its three MLAs V S Sivakumar, Parackal Abdulla and M Jayaraj in the portals of the House since the past eight days over the prohibitory orders in Sabarimala.
Leader of the Opposition in the state Assembly Ramesh Chennithala and former chief minister Oommen Chandy addressed the workers.