Meanwhile, Kim Sook, South Korea's chief envoy to international nuclear talks with North Korea, told reporters in the capital Pyongyang that North Korea would "immediately return to disabling work" at its Yongbyon nuclear facility.
Pyongyang halted the disablement in mid-August in anger at the US over what it called a delay in the terror delisting.
It also began moves aimed at potentially restarting the plutonium-producing facility north of Pyongyang.
The removal from its terror blacklist is provisional, and North Korea will be put back on the list if it does not comply with the inspections, the AP news agency reported, citing diplomats.
The delisting came after days of intense internal debate in Washington and consultations with US negotiating partners.
But Japan's finance minister branded the decision to delist North Korea "extremely regrettable", Japanese media reported on Sunday.
"It's extremely regrettable, and I believe abductions amount to terrorist acts," Shoichi Nakagawa told reporters in Washington at the G7 meeting of finance ministers.
|North Korea's Yongbyon nuclear complex has been at the heart of the controversy [EPA]
"I don't think the United States made the decision after a close consultation with its ally Japan."
Christopher Hill, the chief US negotiator, returned from a trip to North Korea to discuss the issue last week.
Hill met North Korean officials for talks in Pyongyang and it was there that a breakthrough was achieved, South Korea's Chosun Ilbo newspaper quoted a key government official in Seoul as saying.
Monica Villamizar, reporting for Al Jazeera in from Washington, said "it is an unprecedented agreement and very surprising" because of North Korea's recent expulsion of nuclear inspectors and testing of missiles.
Sean McCormack, the US state department spokesman, said North Korea would be required to halt and reverse its recent actions.
"We would hope and expect that if the process is going to move forward, that they take active steps to reverse what they have done over the past month," he said.
But Villamizar said that Washington would not be completely happy with the deal.
"What they expected in the first place was that North Korea would let them inspect any facility at any moment they wanted - so even surprise inspections," she said.
Barack Obama, the Democratic US presidential nominee, said that the move was a "modest step forward" and the US should re-impose sanctions and suspend energy assistance if North Korea does not fulfil its commitments.
John McCain, the Republican presidential nominee, said on Friday, before the official announcement of the delisting, that the denuclearisation had to be stringently enforced and an agreement not made for its own sake.