Seoul attached no conditions to the aid delivery, according to the text of an agreement reached in the early hours of Sunday after five days of economic aid talks in the North Korean capital.
However, South Korea's chief delegate, Chin Dong-soo, later stressed that the rice shipments were contingent on whether North Korea makes move to implement a nuclear disarmament deal reached in February.
Seoul told Pyongyang the rice shipments "cannot proceed as agreed upon without a condition that the North sincerely implements the (February) agreement, that we would have to link the timing and speed of rice aid shipments," Chin told reporters in Pyongyang, according to pool reports.
The first batch of rice will be sent in late May, the agreement said. Seoul will send 350,000 tons by sea, and the remaining 50,000 tons be driven over land, across the world's most heavily fortified border.
North Korea failed to meet an April 14 deadline to shut its Yongbyon nuclear facility over a delay in the release of its funds — US$25 million (euro18.6 million) — frozen in a Macau bank blacklisted by the United States for allegedly assisting the North with money laundering and counterfeiting.
Washington and the bank, Banco Delta Asia, said earlier this month that the North's accounts were no longer frozen, but North Korea, for unknown reasons, has yet to withdraw the money.
Pyongyang on Friday reaffirmed its commitment to the disarmament pledge, but said it was still waiting to confirm that its funds had been released.
South Korea's chief delegate to nuclear talks, Chun Yung-woo, will travel to Washington on Monday to discuss with U.S. officials the nuclear impasse, an official at the Foreign Ministry said Sunday on condition of anonymity due to protocol.
South Korea had been attempting to use the promise of food aid as leverage to pressure the North to honor its pledge to begin to dismantle its nuclear program under the Feb. 13 nuclear deal with the U.S. and its regional partners.
Following the February accord, Seoul decided to resume the aid shipments that it had suspended after Pyongyang conducted missile and nuclear tests last year.
But fearing it could be criticized for lavishing aid on North Korea before it takes steps to disarm, the South had sought to delay actual shipments until the North made progress on the nuclear deal.
Seoul is a key aid donor to the North, has sent more than two million tons of rice to the North since the mid-1990s when natural disasters and mismanagement devastated its economy and led to a famine estimated to have killed some 2 million people.
Also Sunday, the Koreas agreed to test a railway service to run on rebuilt rail tracks across their shared border. The North promised it would try to convince its military to guarantee the safety of travelers during the rail tests on May 17.
Last year, the North unilaterally called off a similar planned test run, citing objections from its military.
Even though the North has canceled similar planned test runs in the past, "the possibility that it will be held is higher than ever," Chin said.
The two sides also agreed that South Korea would send raw materials for making clothes, shoes and soap to North Korea, and in exchange the South would have the right to develop mineral resources in the North.