The incursion took place three times overnight yesterday and at one point the North Korean naval vessel had reached two miles inside the South side of the border.
No shots were fired and the patrol boat eventually retreated after warnings from the South Korean navy, defence ministry spokesman Kim Min-Seok said.
"We suspect this is aimed at testing our military preparedness", Kim told reporters.
North Korean violations of the maritime border - which it does not officially recognise - are not unusual, but this was the first such incident this year.
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The war ended in an armistice instead of a peace treaty and technically, the two Koreas are still at war.
The start of the South-US drills overlapped with the first reunion for more than three years of families divided by the Korean War - an event that has raised hopes of greater North-South cooperation.
The annual "Key Resolve" and "Foal Eagle" drills will last until April 18 and involve a combined total of 12,700 US troops and many more from South Korea.
Last year's drills fuelled an unusually sharp and protracted surge in military tensions, with Pyongyang threatening a pre-emptive nuclear strike, and nuclear-capable US stealth bombers making dummy runs over the Korean peninsula.
US defence officials have indicated - in an apparent effort to mollify the North - that this year's drills will be slightly toned down, with no aircraft carrier and no strategic bombers.