Fumio Kishida said he had called China's ambassador to protest against the "incursions".
On Friday, about 230 Chinese fishing boats and coast guard vessels sailed near islands claimed by both countries.
Beijing has been increasingly assertive about waters it believes are Chinese.
The Japan-controlled, uninhabited islands - known as the Senkaku in Japan and the Diaoyu in China - are the source of a long-running dispute.
