The family members, who arrived here from Kozhikode, were to stage a protest in front of DGP Loknath Behara's office this morning demanding the arrest of all those responsible for Jishnu's death, police said.
As they were walking up to the DGP's office, police prevented them saying it was a restricted area.
Jishnu's uncle alleged that police kicked him and assaulted his sister, Mahija, mother of Jishnu, who lay on the road and protested.
Jishnu's mother, who suffered some injuries, has been hospitalised.
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Meanwhile, the CPI(M)-led LDF government has come under criticism from various quarters for the police action.
CPI(M) veteran V S Achuthanandan called up DGP and expressed his displeasure at the developments.
Leader of Opposition in the Kerala assembly, Ramesh Chennithala said he was "pained" at the government failure to understand the sorrow of a mother, who had lost her only child.
Chennithala, a former home minister, said he was shocked at the arrest of the boy's relatives, while former Chief Minister, Oommen Chandy termed the police action as "shameful."
Various youth organisations are protesting in front of the hospital where Mahija is admitted.
Jishnu Pranoy, a first year student of Nehru college of engineering in Thrissur, was founding hanging in the college hostel in January last, after college authorities harassed him after he was allegedly caught copying in an exam.
Yesterday, Chairman and Managing Trustee of Nehru group of Institutions, P Krishnadas was arrested and let off on bail.
Meanwhile, DGP Loknath Behara visited Mahija at the hospital and enquired about her health.
Later, he told reporters that IGP has been asked to enquire into the violent incidents and file a report by evening.
"I am a law enforcement officer, I have given orders to IGP to enquire and file a report by this evening," he said.
Behara said according to intelligence reports there were some outsiders in the group of family members at the time of the incident. The family wanted to discuss the case with him... SIT is looking into it.
However, there are some "shortcomings," which is why the family wanted to meet him, he said.