Taiwanese ships and protesters entered waters near the islands on Monday after a Taiwanese boat sank a week earlier following a collision with a Japanese coast guard vessel.
Japan says the captain of the Taiwanese ship was responsible for the collision.
Both Taiwan and mainland China claim the islands as Chinese territory.
Ma, who took office in May, said Taiwan was determined to defend its claim to the islands and demanded an apology from Japan over the collision.
Ma's predecessor, Chen Shui-bian, took a much softer line on the issue, seeking friendly relations with Japan and toeing an ambiguous line on Taiwan's claim to the disputed islands.
The value of the islands, situated about 2,000 km southwest of Tokyo, has grown in recent years following the discovery of potentially rich gas reserves in the area.