Seoul has denied the allegations, saying the ship was merely searching for a North Korean fishing boat that was drifting near the inter-Korean sea border
A row between Seoul and Tokyo escalated on Friday after Japan released a video it said backed up its claim that a South Korean warship had locked a weapons targeting system onto a Japanese plane.
South Korea condemned the release of the footage and reiterated its rejection of the Japanese allegations.
Tensions have flared since Japan claimed a South Korean destroyer last week aimed its fire-control radar at a Japanese maritime patrol plane in the sea off the eastern coast of South Korea.
Seoul has denied the allegations, saying the ship was merely searching for a North Korean fishing boat that was drifting near the inter-Korean sea border.