"The BSF seized the Pakistani boat at Harami Nala area in Kutch during routine patrolling," the official said on condition of anonymity, without giving out any further detail.
He said the boat was found at the tri-junction post inside the Indian territory.
According to BSF sources, they have intensified vigil in the area after the incident, to foil infiltration bid, if any.
In a similar incident last month, a Pakistani boat was found abandoned near the Harami Nala area.
Both India and Pakistan are engaged in a political battle over this area, which may be rich in oil and gas, and the brackish water which makes for good fishing grounds.