Ministry spokesman Kim Nam-sik said earlier the first shipment will be 5,000 to 10,000 tons.
Last week Seoul announced its intention to launch fuel oil deliveries within the next two weeks in a bid to supply Pyongyang with 50,000 metric tons within 20 days.
Fuel supplies were a condition for Pyongyang to begin undertaking measures as part of the first stage of its denuclearization. South Korea is expected to deliver 50,000 metric tons of fuel oil first, to be followed by another 950,000 metric tons from the United States, Russia and China.
Japan refused to join the assistance program until the problem of its nationals kidnapped by North Korean security services in the 1970s-1980s is solved.
The latest reports said Japan also opposed South Korea's intention to launch fuel oil supplies until Pyongyang shuts down its nuclear reactor.
Japanese Cabinet spokesman Yasuhisa Shiozaki insisted Wednesday that international assistance and the closure of the reactor be carried out in parallel, though North Korea had asked for assistance first.