Strongly objecting to the government decision, the opposition members comprising Congress-led UDF, Kerala Congress (M) and the lone BJP legislator staged a walkout.
Opposition leader Ramesh Chennithala said they would challenge the matter in court and termed the government decision as a jolt to democracy and "dark chapter.'
Replying to a notice for an adjournment motion sought by the UDF on the matter, Vijayan justified the government's decision and said there was no impropriety in it.
Vijayan said it was done to uphold the rights of the House and the government does not want to handover its power to another institution (judiciary).
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The constitution has clearly defined rights and powers to the three pillars of democracy -Legislator-Judiciary and Executive.
"It will be not be prudent to take matters that occurred in the House to the court," he said.
The decision was taken upholding the spirit of the constitution.
The Chief Minister said the previous UDF government acted indiscriminately as they did not file a case on a petition filed by four LDF women MLAs that they were molested and manhandled by UDF members.
The case against the six LDF MLAs was taken based on a complaint filed by the Assembly Secretary without the approval of the House and also its leader, Vijayan said.
Slamming the government over the issue, Chennithala said what the then LDF legislators had done was a criminal offence and "they have to face trial in the court."
Seeking notice for the motion, V D Sateeshan (Cong) said the legislators' action was actually an offence against the state. "They have to face trial," he said.
The assembly had witnessed unprecedented and ugly scenes on March 13, 2015 as opposition LDF members tried to prevent then finance minister K M Mani, who was facing charges in the bar bribery scam, from presenting the state budget.
Besides flinging the Speaker's chair from the podium, electronic equipment like computers, keyboard and mikes on the desk of the presiding officer were also damaged by LDF members.
Sivankutty last month wrote to the chief minister and assembly speaker P Sreeramakrishnan, seeking withdrawal of the police case against him and five other LDF members, alleging that it was "politically motivated."
Of them K T Jaleel is the state minister for Local Self-government in the present LDF government and E P Jayarajan, an MLA.
The case was registered during the previous UDF rule against the six LDF mlas under relevant sections of Prevention of Destruction of Public Property Act and IPC sections 447 (criminal trespass) and 427 (mischief causing damage).
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