Police said some protesters showed black flags to the chief minister's vehicle near the Cantonment Gate of Secretariat, the administrative hub, at the heart of the city.
The protesters were immediately taken away by the police.
Tension prevailed in front of the Secretariat after some protesters blocked the movement of Forest Minister K Raju's vehicle in the morning as part of the hunger strike of Youth Congress state president Dean Kuriakose, along with another activist Mahesh, which entered the fifth day.
Reacting to the incident, Raju later said it was "quite unexpected" and should not have happened. He also claimed that the protesters banged on his car and waved black flags.
In a similar incident in the northern district of Kannur, a group of Youth Congress activists showed black flags to state Health Minister KK Shylaja, police said.
Meanwhile, two Congress MLAs -- K Sabarinathan and M Vincent -- staged a dharna in front of a police station demanding immediate release of party workers, taken into custody in connection with the incidents.
Chandy demanded a probe into the incident while Chennithala alleged that the police acted against the protesters "without any provocation".
The Youth Congress was demanding scrapping of the agreement between the state government and the managements of private self-financing medical colleges, maintaining that the new fees structure was "very high" and alleging corruption.
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