"The North's request to several companies for a schedule of people returning to the South by April 10 has been distorted to say the North had requested a total pullout," the Unification Ministry said.
An executive with the association of the 123 companies that operate in Kaesong, Ok Sun-suk, told reporters earlier that the North had ordered South Koreans to pull out by April 10.
North Korea barred entry to a joint industrial complex it shares with the South for a second day on Thursday, the South Korean Unification Ministry said, but would allow 222 South Korean workers to leave the zone through the day.
However, after the 222 South Korean workers leave between 10 a.m. and 5 p.m. (0100-0800 GMT), another 606 South Korean workers will remain in the Kaesong complex.
North Korea has threatened to shut the complex, one of the impoverished North's few sources of ready cash, as part of a tense standoff with Seoul and Washington.
"222 South Korean workers will leave (Kaesong) at the time of their choice along with 131 vehicles," said Park Soo-jin, a spokeswoman at the ministry. The gates between North and South Korea will open for the workers 10 times on Thursday.
The ministry is in charge of handling inter-Korean affairs.
South Korea has had to submit a list of those wishing entry to the complex three days in advance since North Korea shut all of its official communication lines with South Korea, the United States and the United Nations last month.
The South Korean government has urged its citizens to leave the zone.
South Korea's defence ministry said Wednesday it had contingency plans, including possible military action, to ensure the safety of its citizens working in a joint industrial zone in North Korea.
"We have prepared a contingency plan, including possible military action, in case of a serious situation," Defence Minister Kim Kwan-Jin told ruling party MPs in a meeting.
"We should try to prevent the situation from going to the worst," Kim added.
North Korea blocked South Korean access to the Seoul-funded Kaesong joint industrial zone on Wednesday, but said it would allow the 861 South Koreans currently there to leave.
As of 2:00 pm (0500 GMT) only nine had crossed back over the border into South Korea.
The South's Unification Ministry said many had voluntarily opted to stay in Kaesong to ensure the smooth operation of their companies there.
South Korean workers were denied access to an industrial park jointly run with North Korea for the first time since 2009, a spokeswoman for South Korea's Unification Ministry said.
Contact is made daily with North Korea at 8 am to allow South Korean workers to enter the Kaesong industrial zone. On Wednesday, no response had been received as of 9.30 am, local time.
A South Korean official said hundreds of South Koreans currently in the Kaesong Industrial zone would be allowed to leave.
North Korea had earlier delayed access to the park.
The zone generates $2 billion a year in trade for the impoverished North.
Voice of Russia, Reuters, Bloomberg, AFP