(Edits, Adds South Korean fuel aid to North)

By Chris Buckley

BEIJING, June 30 (Reuters) - The U.N.'s nuclear watchdog has clarified how to monitor the shutdown of North Korea's nuclear facility and it is now up to Pyongyang and its five negotiating partners to decide on a date, an official said on Saturday.

International Atomic Energy Agency (IAEA) official Olli Heinonen said negotiations in North Korea had achieved an understanding on how to monitor the sealing and shutdown of the Yongbyon facility.

But he stressed the timing of the long-negotiated shutdown needed consultation between North Korea and other countries in six-party talks to iron out the details.

"The next logical step is that they talk with each other and agree on technical arrangements. The IAEA doesn't have any role on that," Heinonen, IAEA Nuclear Safeguards Director told reporters in Beijing after several days of talks in Pyongyang.

"I think that they will take the shutdown as soon as they agree with their partners about the timing," he added later.

North and South Korea, the United States, Japan, Russia and host China struck a deal on Feb. 13 under which Pyongyang would receive aid and security steps in return for moving to scrap its nuclear arms programmes.

The IAEA, as the guardian of international nuclear safeguards, will monitor and verify the disarmament steps.

The deal was stalled for weeks by a dispute over some $25 million in North Korean funds frozen in a Macau bank under pressure from Washington. Following the release of the funds, North Korea agreed to implement the deal.

AID TO FLOW

South Korea will begin shipping 50,000 tonnes of heavy fuel oil in two weeks and try to complete the supply in 20 days, its unification ministry said, after two days of talks with the North on the details of the energy aid.

North Korea is set to receive another 950,000 tonnes of fuel oil or other aid of equivalent value when it completes steps to disable all its nuclear facilities under the Feb. 13 deal.

Heinonen said he had visited five "major facilities" at the Yongbyon complex, about 100 km (60 miles) from the capital.

It was the first trip by an IAEA official to the facility -- whose working reactor produces plutonium, which can be processed for nuclear weapons -- since Pyongyang kicked out the Vienna-based agency in December 2002.

After expelling the inspectors, North Korea left the nuclear Non-Proliferation Treaty, indicated it had atomic weapons and last year conducted its first nuclear test explosion.

In South Korea on Saturday, an official said the first shipment of rice aid to North Korea in two years had been sent to the North after it pledged to begin implementing the nuclear disarmament deal.

South Korea refused to give the aid last year after the North defied international warnings and test-fired a barrage of missiles in July and deepened tensions with its first nuclear test in October. The last shipment was sent in December 2005. (Additional reporting by Mark Chisolm in Beijing and Jack Kim in Seoul))

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