The two sides clashed seriously in 2002
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North Korea has accused South Korea of "grave provocation" after the South fired warning shots at its vessels.
In a statement published by the official KCNA news agency, North Korea said an armed clash was only avoided thanks to its navy's restraint.
The criticism referred to an incident on Monday, when a South Korean warship fired shots at boats which it said had crossed into Southern waters.
But the North has insisted its boats were on a routine patrol.
"The South Korean armed forces deliberately committed this armed provocation which may give rise to another skirmish," the North's statement said.
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TROUBLESOME BORDER
Known as Northern Limit Line
Position declared by UN in 1953
Not recognised by North
Regularly breached by North's fishermen
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"Such military provocation... is an unpardonable provocation and a
blatant challenge to the North in the light of the present
inter-Korean relations," it continued.
It was thanks to "the high restraint and
patience" exercised by North Korean seamen that the incident did not spark
"a grave armed conflict", Pyongyang insisted.
This is the latest in a series of incidents along the border between the two Koreas, and around the coast of the peninsula.
Naval clashes in 1999 and 2002 left several people dead, and led to both sides agreeing new measures to reduce tensions.
These measures included a telephone hotline and sharing radio frequencies.