Chief Minister Manohar Parrikar said that the alert 'was of a general nature'.
The captain of ports, Goa government's department dealing with the ships, on Tuesday asked the fishing community to be alert.
Besides the fishing vessels, which are currently on shore due to the ongoing fishing ban, the off shore casinos anchored in Mandovi river are also put on alert.
Police are coordinating with the Indian coast guard and the Navy on the issue, a senior official said.
Alert was sounded off in the Konkan region of Maharashtra too the alert is sounded, Superintendent of Police, Sindhudurg (Maharashtra), Abhishekh Trimukhe said. He held a meeting on security issues with his Goa counterparts.
The intelligence gathering has been heightened along the coast, he said.
"We are in touch with Indian Coast guard on regular basis. The patrolling on the beaches has also been increased," Trimukhe added.