North Korea invited the IAEA to return after a dispute over assets frozen in a Macau bank two years ago was finally resolved.
Russian foreign ministry confirmed on Saturday that the money had been transferred into a private Russian bank.Disarmament deal
North Korea said on Saturday it would begin implementing the disarmament deal agreed in February as soon as it recovered the Macau funds.
Under that agreement, hammered out after a surge in tensions following the North's first nuclear weapons test last year, Pyongyang promised to close the plant in return for energy aid and diplomatic concessions.
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In the communists state's first substantive comments since Hill's visit, a foreign ministry spokesman also said the the two sides had agreed to resume six-party talks on dismantling the nuclear programme early next month.
"The discussions were comprehensive and productive," the spokesman was quoted as saying by the official Korean Central News Agency.
Hill said that the next round of talks between the US, China, Japan, Russia and the two Koreas would get under way after the reactor was closed.
Beginning of the process
But he also said that closing the facility was just the beginning of the process.
"Shutting down the reactor does not solve all our problems," he told reporters in Tokyo.
In Pyongyang, Hill met Pak Ui-Chun, North Korea's foreign minister, and Kim Kye-Gwan, its chief envoy to the six-party talks that drew up the February 13 accord.