Forensic identification tests in Hawaii confirmed they belong to South Korean war dead, according to Seoul's Defense Ministry.
At a summit with the South's President Moon Jae-in last month, the North's leader Kim Jong Un offered to shut down its main Yongbyon nuclear complex if Washington takes "corresponding measures".
A South Koren defence ministry spokesperson said the operation had begun on both sides, though there has been no confirmation by the North.
The KCNA said North Korea has taken "substantial and crucial steps" to implement the summit agreement with the U.S. but that Washington is still talking about intensifying sanctions, rather than trying to resolve the end-of-war declaration issue that should have been resolved decades ago.
The official refused to provide more details. But Trump, Pompeo and other USA officials have recently reported progress in denuclearization discussions with the North. Pompeo is to make his third trip to North Korea soon.
In a statement, the ministry said the two sides agreed to remove all landmines in the so-called Joint Security Area (JSA) in Panmunjom within the next 20 days, with military engineers performing the hazardous task on the South Korean side.
As part of last month's deal, guard posts and weapons will be shipped out of the JSA after the demining. The US has said that it will not make such concessions unless the North takes substantive steps in ridding itself of nuclear weapons.
In 2015, a land mine blast blamed on North Korea maimed two South Korean soldiers and pushed the Koreas to the brink of war.
At Arrow Head Hill, where some of the fiercest battles occurred during the Korean War, Seoul officials believe there are remains of about 300 South Korean and United Nations forces, along with an unspecified number of Chinese and North Korean remains.
The Koreas remain split along the 248-kilometer (155-mile) -long DMZ that was originally created as a buffer zone at the end of the Korean War. It is believed that there are tens of thousands of landmines in the two areas to be cleared.
Meanwhile, South Korean President Moon Jae-in expressed optimism, claiming recent agreements will end all hostile acts.
The commentary Tuesday by the North's official news agency said a declaration replacing a 65-year-old armistice to formally end the war "is not just a gift from a man to another", and added, "it can never be a bargaining chip for getting the DPRK denuclearized".