The move raises the prospect of the permanent closure of the Kaesong complex, the last point of contact between the two Koreas and a key source of income for Kim Jong-Un's isolated regime.
South Korean companies with factories at the site have expressed shock at the sudden evacuation, which saw 126 workers return on Saturday in dozens of vehicles loaded with assembled goods and other materials.
The roughly 50 people remaining -- mostly government employees who manage the site, as well as telecom and electrical engineers -- are due to cross back at about 0800 GMT on Monday, according to Seoul.
"We notified the North about the planned return of 50 people today but have not received approval from the North yet," Unification Ministry spokesman Kim Hyun-Seok told reporters.
But he noted that on Saturday North Korea had granted approval just 30 minutes before the workers were scheduled to depart.
Seoul announced on Friday that it had decided to pull all remaining employees from Kaesong after Pyongyang blocked access to the site and refused to open talks on restarting the stalled operations.
The complex is the victim of escalating tensions triggered by a nuclear test by the North in February, which has been followed by a series of bellicose threats of nuclear war and missile tests by Kim Jong-Un's regime.
South Korean Foreign Minister Yun Byung-Se told a forum in Seoul on Monday that "the window of dialogue is still open" on Kaesong, according to the South's Yonhap news agency.
"North Korea must understand that its missile and nuclear programmes are just an empty dream," Yun added.
But some observers believe the shutting down of the complex would be permanent as the factory equipment there would fall into disrepair and the firms would soon lose their customers.
"Some people say that the complex may be reopened in a few weeks or months once the two sides hammer out a deal, but it's a ludicrous idea," said Yang Moo-Jin, a professor at the University of North Korean Studies in Seoul.
"Once the complex dies, the North will naturally deploy its troops back there, returning the military situation to the pre-Kaesong days. All the artillery units targeting Seoul will move closer to the border, which will surely heighten military tension," he told AFP.
Pyongyang, which has demanded the end of UN sanctions and a halt to all South Korea-US joint military exercises, announced on April 8 that it was pulling out its 53,000-strong workforce from Kaesong, angered by the South's mention of a "military" contingency plan to protect its staff at the site.
Established in 2004, the complex lies 10 kilometres (six miles) inside the North, which remains technically at war with the South after the 1950-53 Korean War was concluded with a ceasefire rather than a peace treaty.
The North on Monday renewed its own threat of "final and decisive" action on Kaesong if the situation worsens.
The pullout is "a cunning and mean-spirited trick aimed at passing blame to the North for the plight of the complex", said an editorial in the North's ruling communist party newspaper, the Rodong Sinmun.
"The enemy forces should know clearly that we, as warned already, will take any final decisive and crucial measures if they continue to try to aggravate the situation," it said.
Yonhap reported on Sunday that North Korea appeared to be preparing for a major live-fire military exercise on its west coast involving artillery units and air force jets.
Joint South Korea-US military drills which have angered the North are due to end on Tuesday.