There are only eight Indian fishermen in Sri Lanka, he said.
Senaratne said the problem pertaining to the intrusion would be sorted out through discussions between the two sides.
The two governments and fisheries cooperatives and unions have agreed to a negotiated resolution of the recurring problem.
Recalling the past flurry of diplomatic activity between New Delhi and Colombo on the issue of fishermen straying into each other's waters, the minister said Sri Lanka had turned down a request made by India to allow its fishermen to fish in Sri Lankan waters for a limited period.
The fisheries ministry officials, commenting on the recent arrest of six Sri Lankan fishermen by Indian coast guards, said negotiations were underway to secure their release.
The issue of fishermen has led to high-level diplomatic contacts between the two nations, including the appointment of a joint commission last year to tackle the problem.
Sri Lanka's minister from the northern Jaffna district Douglas Devananda had last month threatened to take a group of fishermen to protest in India and urge the Indian authorities to prevent Indian fishermen from "violating" the international maritime border limits across the Palk Strait, the narrow sea strip between India and Sri Lanka.