The goods, including 6,400 tons of cement, were shipped to the North Korean port of Nampo, said the Unification Ministry, which handles North Korean affairs.
"As North Korea has yet to conduct a nuclear test, it is difficult to immediately halt sending flood relief aid, which is being provided on a humanitarian basis," a ministry official said on condition of anonymity, citing official policy.
"However, we will decide future plans (of shipments) after monitoring the situation," the official said.
North Korea alarmed its neighbors Tuesday by announcing that it plans to conduct its first nuclear test. The communist country says it has atomic bombs, but has not held any known test to prove its claims.
Wednesday's shipment was part of emergency assistance that Seoul promised the North after the communist nation was hit by massive floods in July.
South Korea has said the one-time aid is separate from the regular humanitarian aid to the North it has halted since missile launches by the North in July.