The agency said it fired water cannon at some boats whose crew refused orders to leave the Yamato Banks, a rich fishing ground in the Sea of Japan (East Sea), adding that the expulsions started in mid-July.
It was the first time the coastguard revealed it has being booting the North Korean ships from Japan's exclusive economic zone (EEZ).
The announcement came two days after North Korea launched a missile over Japanese territory, drawing global condemnation and stoking calls for more sanctions against the regime.
The agency added that a particular boat might have received more than one warning.
"Since mid-August, we haven't seen North Korean fishing vessels in waters around the Yamato Banks," an agency official said.
Every year, badly damaged boats -- sometimes with rotting corpses inside -- wash up on Japan's shores.
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