The Sena activists, who had demanded cancellation of Ali's programme in the wake of the Pathankot terror strike linked to Jaish-e-Mohammed, were stopped nearby the venue by the police.
Water cannons were used to disperse around 200 Sena activists who burnt a Pakistan flag as a mark of protest, police said.
Ali, whose concert in Mumbai had to be cancelled last year following protests by the Sena, was accorded a public reception here yesterday, attended by a galaxy of state leaders, including state Chief Minister Oommen Chandy.
He is in Kerala at the invitation of socio-cultural organisation 'Swaralaya'. The programmes were arranged in association with Grand Kerala Shopping Festival Directorate.