Seoul's Unification Ministry, which is in charge of relations with the North, called the move an "unhelpful measure for the safe operation of the Kaesong complex."
The Unification Ministry said only three telephone hotlines remain between the North and South, and those are used only for exchanging information about air traffic.
South Korean officials said about 750 South Koreans were in Kaesong on Wednesday, and that the two Koreas had normal communications earlier in the day over the hotline when South Korean workers traveled back and forth to the factory park as scheduled.
Workers at Kaesong could also be contacted directly by phone from South Korea on Wednesday.
A South Korean worker for Pyxis, a company that produces jewelry cases at Kaesong, said in a phone interview that he was worried about a possible delay in production if cross-border travel is banned again.
"That would make it hard for us to bring in materials and ship out new products," said the worker, who wouldn't provide his name because of company rules.
The worker, who has been in Kaesong since Monday, said he wasn't scared.
"It's all right. I've worked and lived with tension here for eight years now. I'm used to it," he said.
Kaesong is operated in North Korea with South Korean money and know-how and a mostly North Korean work force. It provides badly needed hard currency in North Korea, where many face food shortages.
Other examples of joint inter-Korean cooperation have come and gone. The recently ended five-year tenure of hard-line South Korean President Lee Myung-bak saw North-South relations plunge. Lee ended an essentially no-strings-attached aid policy to the North.
North Korea last cut the Kaesong line in 2009, in a protest of that year's South Korean-U.S. military drills. North Korea refused several times to let South Korean workers commute to and from their jobs, leaving hundreds stranded in North Korea. The country restored the hotline and reopened the border crossing more than a week later, after the drills were over.