South Korean Defense Ministry spokesman Kim Min-seok said that the navy Monday night spotted a North Korean warship straying into the South Korean waters.
There have been many reported violations by North Korea previously. But the timing of the latest incident has raised tension in the region.
The latest incursion came on the first day of the US-South Korean war games, which are one of the largest military exercises conducted by the two countries, with nearly 200,000 troops from both countries taking part.
North Korea calls the joint military exercises a rehearsal for a possible attack. But the US and South Korea say they are for purely defensive purposes.
North Korean state media Monday protested the exercises.
Kim said a 420 metric-ton vessel made three cross-border trips inside 13 nautical miles (15 miles) west of South Korea's Yeongpyeong Island, which is off the west coast of the Korean peninsula. After repeated trips, the vessel left at around 2 a.m.
The warship was warned not to cross maritime boundaries but it didn't respond and continued foraying into South's waters, he said.
"The North Korean ship's NLL [Northern Limit Line] violation is seen as part of military drills or an inspection of [South Korean military]. It is believed that [the North Korean vessel] intended to test the South Korean military," spokesperson Kim told reporters.
"There wasn't an exchange of fire, though."
The South Korean spokesman said that they were "closely looking into possibilities that the North Korean intentionally violated the NLL".
"The military decided to make public [the alleged incursion] because people have a lot of interest in the North Korean military's moves."
The maritime border, called the Northern Limit Line, is contested by North Korea. The maritime border remains a contentious issue between the neighbours as the boundary was unilaterally created by UN forces subsequent to the 1950-53 Korean War. The region had occasionally witnessed skirmishes.
The area has in the past been the site of deadly naval clashes in the past. Fishing boats and patrol vessels from North Korea often ignore the line of demarcation.
In November 2010, North Korea shelled Yeongpyeong island, killing two soldiers and two civilians. A South Korean warship was sunk earlier that year near another island along the Northern Limit Line, killing 46.
An international investigation concluded that a North Korean torpedo was responsible. North Korea disputes the investigation's findings.