South Korean President Lee Myung-Bak warned on Monday of "growing threats" to the country's maritime security, posed by North Korea and regional territorial disputes over isolated island chains.

South Korean naval patrol boats fired warning shots on Friday at six North Korean fishing boats that crossed the disputed Yellow Sea border, the latest in a series of similar incursions.

It was the first time for two years that the South has resorted to firing warning shots to push the fishing boats back.

None of the vessels were hit and they swiftly returned to their side of the western sea boundary. The North said any incursion was made by the South's navy and threatened military retaliation.

Speaking at a coastguard base in the southern port city of Busan, Lee said threats to the South's sovereign waters were "growing day by day".

"We can never let our guard down even for a moment amid continued maritime threats by North Korea and rising tension on the seas of Northeast Asia," Lee said.

Earlier on Monday, Seoul's pointman in cross-border ties said the repeated incursions by North Korean fishing vessels might be a deliberate ploy by Pyongyang to provoke South Korea.

"Too many ships are violating the border too many times to call them a mistake," Unification Minister Yu Woo-Ik told reporters.

Friday's incident occurred close to the South's Yeonpyeong island, which the North shelled in 2010, killing four South Koreans, including two civilians.

The disputed sea border off the west coast was the scene of deadly naval clashes in 1999, 2002 and 2009.

The de-facto maritime boundary between the two Koreas -- the Northern Limit Line -- is not recognised by Pyongyang, which argues it was unilaterally drawn by the US-led United Nations forces after the 1950-53 Korean War.

In his remarks to the coastguard, Lee also praised its role in securing control over a group of rocky islets located in the sea between South Korea and Japan and claimed by both countries.

Known as Dokdo in Korean and Takeshima in Japanese, tensions over ownership escalated sharply after Lee made the first-ever presidential visit to the islands last month.

"I felt so relieved having seen your firm determination to protect our sea with your lives when I visited Dokdo," Lee said.

Japan is currently involved in another high-stakes standoff with China over a separate group of islands, these in the East China Sea, which both countries claim sovereignty over.

A decision by the Japanese government to buy three of the islands from their private owners earlier this month triggered violent anti-Japanese protests in China.