"They are now under investigation by the institution."
The announcement comes a day after Pyongyang accused South Korea and the US of planning a surprise attack with their joint military exercises.
Most South Koreans working on the northern other side of the heavily-guarded border are employed at the jointly-run Kaesong industrial estate.
It is the third time in two months the North has reported an illegal border crossing.
Robert Park, a US missionary, walked into the North across the frozen Tumen river from China on December 25 to draw attention to its human rights abuses.
|North Korea has condemned South Korean-US exercises due to be held next month [EPA]
He was freed on February 6 after expressing what the North described as "sincere repentance".
Pyongyang also said on January 25 that it was holding an unidentified American for illegal entry from China.
The person's motives are unknown and US officials have not confirmed the detention.
North and South Korea have been divided for decades by barbed wire and minefields, making any illegal entry from the South very difficult.
On Thursday meanwhile, the North Korean army described US-South Korean military exercises to be held next month as "pilot operations and nuclear war exercises" aimed at mounting a surprise pre-emptive attack on the North.
The military said it would retaliate for any attack "with our powerful military counteraction, and if necessary, mercilessly destroy the bulwark of aggression by mobilising all the offensive and defensive means including nuclear deterrent".
Amid the ongoing tensions, diplomatic efforts continue aimed at persuading the North to return to stalled nuclear disarmament talks.
Stephen Bosworth, the US envoy to North Korea, was to leave for Japan on Friday after talks in China and South Korea aimed at reviving the six-nation dialogue.
North Korea quit the talks last April, shortly before it conducted a second nuclear test and tested a long-range rocket.