The news agency, citing an unnamed source, said the talks began at 10:00 at the truce village of Panmunjom in the Demilitarized Zone.
In recent weeks the two Koreas have exchange limited gun fire across both their land and sea borders.
South Korean ministry officials have not formally confirmed the talks.
Yonhap, citing its parliamentary source, said it was because North Korea did not want the talks made public.
An opposition lawmaker gave the same information to a party meeting, a statement from his party said.
The talks were widely expected to focus on reducing tensions after two small military incidents across the border that divides the two nations – which remain technically at war.
Last week, gun fire was exchanged after a North Korean patrol ship crossed the disputed western maritime border, South Korea said.
On October 10, there was also an exchange of fire across the land border, something that happens rarely.
South Korea’s Yonhap news agency, citing military officials, said North Korea fired towards balloons carrying propaganda leaflets that had been launched across the border by South Korean activists.
South Korea responded after some shots landed south of the border, its officials said.
The two sides last held working-level military talks in February 2011 and general-level talks in December 2007, Yonhap said.
In February, Pyongyang and Seoul also had two rounds of high-level meetings in Panmunjom, without providing any details on how the talks went.
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