The talks -- delayed by nearly two hours -- follow months of friction and threats of war by Pyongyang after its February nuclear test attracted tougher UN sanctions, further squeezing its struggling economy.
Kaesong was the most high-profile casualty of the elevated tensions on the Korean peninsula but neither side has declared the complex officially closed, instead referring to a temporary shutdown.
Both nations say they want to reopen the Seoul-funded industrial zone on the North Korean side of the border but blame each other for its suspension.
His South Korean counterpart and senior Unification Ministry official, Suh Ho, said: "We've come here with a heavy heart as the Kaesong industrial zone has been shuttered down. I hope we settle the issue through mutual trust and cooperation."
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Pyongyang, citing military tensions and the South's hostility toward the North, in April withdrew its 53,000 workers from the 123 Seoul-owned factories at the Kaesong park.
Technical problems delayed the start of the talks at the border truce village of Panmunjom today as telephone lines to the South needed repairs, the Unification Ministry in Seoul said.
Seoul is expected to call for a written guarantee aimed at preventing a recurrence of the unilateral shutdown, a demand which the North would find it hard to accept as it would amount to Pyongyang swallowing its pride and accepting full responsibility for the suspension.
At an access road to Panmunjom, Suh encountered a group of businessmen with plants in Kaesong. They carried banners expressing hope that the talks would be successful. One read: "We want to work again. Restart Kaesong.