CPI ministers E Chandrasekharan, V S Sunil Kumar, K Raju and P Thilothaman did not attend the cabinet meeting as per a party directive asking them "not to attend the cabinet meet if Chandy took part."
The transport minister later resigned.
CPI, a key partner in the ruling LDF had taken a stand that Chandy should quit the post following allegations of encroachments by his luxury resort in Alappuzha district and Kerala High Court's strictures yesterday.
Confirming that CPI ministers did not attend the meet, Vijayan said that it was an "unprecedented" step which should not have been happened.
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When asked how the issue was going to be resolved, Vijayan quipped that they would attend the next cabinet meeting.
The chief minister said CPI ministers had given him a letter stating that they were keeping away from the cabinet meet as per their party directive.
He further said their action (CPI ministers) cannot be treated as a lack of collective responsibility of the cabinet as they have to abide by their party directives.
Revenue Minister E Chandrasekharan said, "Our party did not have any personal animosity with anybody and we are opposing only the position taken by parties".
The businessman-turned politician had come under attack from the Congress-led UDF and BJP over allegations that his resort at Kuttanad in Alappuzha had encroached upon Marthadom lake and also violated land rules.
In a blow to the ruling Front, Kerala High Court had yesterday severely criticised Chandy for challenging the collector's report holding that a minister cannot file a petition against his own government, which amounted to lack of collective responsibility in the cabinet.
Chandy, a three-time MLA from Kuttanad, had joined the Pinarayi cabinet in April after party nominee A K Saseendran resigned after a sleaze audio with a woman went viral.