A South Korean naval ship fired warning shots Thursday and seized a North Korean fishing boat intruding across the disputed Yellow Sea border, military officials said.

The vessel sailed a nautical mile south of the sea boundary at 5:26 pm (0826 GMT), prompting a South Korean patrol ship to take action, the South's defence ministry said.

"Our side fired warning shots as the North Korean vessel ignored repeated warnings to retreat," a ministry spokesman told AFP.

The vessel with three people aboard was captured about two hours later as it failed to sail back into northern waters probably due to foggy weather and strong currents, he said.

The vessel's crew will be investigated to see whether the incursion was accidental, he said.

The spokesman said a tough response from South Korea was inevitable given the high tensions along the disputed sea boundary.

The South Korean naval ship radioed a message to a North Korea military vessel staying near the sea boundary that the seizure was aimed at ensuring the safety of the crew, he said.

The maritime border, which Pyongyang does not officially recognise, was the scene of brief but bloody naval clashes in 1999, 2002 and 2009.

North Korean incursions over the maritime border are not unusual.

A North Korean patrol boat violated the sea boundary on February 25 at the start of South Korea-US military drills, and retreated after warnings from the South Korean navy.

Thursday's incursion came after nearly 15,000 South Korean and US troops kicked off a 12-day amphibious landing drill, the largest for two decades.

The joint military exercise is taking place off the country's southeast coast. It will last until April 7 and involve around 10,000 US troops.

North Korea views such exercises as provocative rehearsals for invasion and there is a risk they could further fuel already simmering military tensions.

Pyongyang has carried out a series of rocket and short-range missile launches in recent weeks, sparking condemnation from Seoul and Washington.

On Wednesday, it upped the ante by test-firing two mid-range ballistic missiles capable of striking Japan.

United Nations resolutions prohibit North Korea from conducting ballistic missile tests and the UN Security Council was set to hold closed-door consultations Thursday to discuss a possible condemnation of the latest missile launches.