The flags were hoisted to show that the guard posts are to be dismantled in accordance with an agreement reached at a third inter-Korean summit in September, according to the Yonhap news agency.
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"This is aimed at enabling each side to observe the progress in dismantlement work so that it can be carried out in a transparent manner," a defense ministry official was quoted as saying by the agency.
In September, Seoul and Pyongyang signed a military pact that called for a gradual removal of guard posts "on a trial basis" from the Demilitarized Zone (DMZ) separating the two Koreas.