The party's state unit secretary Harikumar criticised Modi's recent visit to Pakistan and said it was done without taking Parliament and people into confidence.
"The latest attack is an example that Pakistan has not changed," he said.
The activists later took out a march in the city in protest against the attack on the airbase and demanded that India sever all relations with Pakistan.
Shiv Sena has no tie-up with BJP and NDA in Kerala.
Seven security personnel were killed in the attack on the airbase.
After operations lasting three days, security forces on Monday killed two more Pakistani terrorists within the air base with the government saying six of them had now been neutralised, but it was not clear whether all the intruders have been eliminated.
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