"Sometime next week, the first shipment of relief materials will possibly be made (to North Korea)," ministry spokesman Chun Hae Sung said in a news briefing.
Since the end of June, torrential rainfall and strong winds have wreaked havoc across North Korea, worsened by the impact of Typhoon Muifa in August, according to the International Federation of Red Cross and Red Crescent Societies.
Ties between the neighbours were aggravated when 46 sailors died in the sinking in March last year of the warship Cheonan, which was blamed on Pyongyang.
North Korea strongly denied involvement in the ship sinking. Relations further deteriorated when the North launched an artillery attack on a South Korean border island last November, killing two Marines and two civilians.
Inter-Korean relations seem to be warming with South Korea on September 2 allowing members of the country's largest Buddhist sect to visit North Korea.
Meanwhile, a US humanitarian aid shipment for recovery from flooding arrived in Pyongyang on Saturday.