At some places, skirmishes were reported between the police and the protesters.
Top leaders of the Congress led the protests in the districts along with party activists in huge numbers.
Leading the protesters in the northern district of Kasargode, state Congress chief Mullapally Ramachandran said they will stick to the party's ideology and stage a non-violent protest.
"This CAA is one that will bring doom to the country, which is already reeling under widespread protests. This is a decision that's going to affect the country in a big way and hence it should be withdrawn," said Ramachandran.
Leader of the opposition Ramesh Chennithala led the protesters at Malappuram. "The CAA would soon be thrown into the dustbin," he said.
"Through this, the Centre has unleashed terror on the citizens of our country and people have risen to the occasion to register their strongest protests," said Chennithala.
In the state capital former Congress President M.M. Hassan opened the protest.
Angry student and youth wing activists of the Congress created a minor stir when they barged into the General Post Office here and the police had a tough time in catching them.
This was the second round of protests by the Congress in Kerala and the next round is going to be a long march by its Lok Sabha members.
( With inputs from IANS )