The 16-feet long boat from Thalaimannar in Sri Lanka was found without an engine, they said.
The incident comes two days after the Marine Police ADGP Vanniyaperumal inspected the security arrangements here.
Police suspect that four to five persons could have arrived by the ferry.
The boat had managed to reach the Indian coast despite round-the-clock vigil by the marine police, they said.
Further investigation is on, police said.
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