They suspected that the boat must be brought early this morning though it was not known who had come in it.
Whoever arrived in the boat had studied the Indian Coast Guard and Marine Police's Patrolling system well and "came here safely", an official of the Intelligence wing said.
The boat has been seized and put under custody of the Coast Guard.
Meanwhile, Indian Navy area Commander Nandi declined to elaborate much on the matter but said a boat had been sighted and it was without an engine.
Besides a general security alert, in view of the threat to the Lord Ramanathaswamy Temple here, was also in force.
According to officials, there was a possibility that some pro-Tamil sympathisers might have come to take part in the unveiling of "Mullaivaikkal Ninaivu Mutram, a memorial for Tamil victims of the 2009 'Eelam war' in Sri Lanka, at Thanjavur yesterday.