The boats were found deserted in Harami Nala area of Kutch district, around 400 km from here, near the Indo-Pak border, BSF said in an official statement.
The occupants of these Pakistan-origin fishing boats may have fled in other vessels after seeing patrolling party approaching them as they were in Indian territory, it said.
They are around 30 feet in length and 5 feet in width and "appear to be normal fishing boats", the statement added.
"BSF seized these boats in Harami Nala area and has started an investigation," it added.