Tokyo had strongly opposed US plans to remove Pyongyang from its list of state sponsors of terrorism due to an emotionally charged row over North Korea's kidnappings of Japanese in the 1970s and 1980s to train its spies.
But the United States has said it will go ahead with the delisting after the communist state hands over a long-delayed declaration of its nuclear programmes as required under a six-nation disarmament deal. This is expected on Thursday.
"This is something that should be welcomed if the nuclear issue starts moving towards resolution," Prime Minister Yasuo Fukuda told reporters, referring to the nuclear declaration.
But Fukuda said the abduction issue should not be neglected.
"We also have the kidnapping issue to resolve," he said. "For that purpose as well, we need to maintain even closer communication with the United States."
While Japanese leaders stayed diplomatic, the US stance caused anger for abductees' families, who had earlier travelled to Washington in an unsuccessful bid to lobby to keep North Korea on the terror blacklist.
"We are deeply shocked," said a visibly angry Shigeo Iizuka, whose sister was snatched by North Korea and who heads an association representing abductees' families.
"We cannot remain silent in a situation like this. We will take our firm position and people's anger straight to the government," he said.
Fukuda, seen as a moderate, last year replaced conservative premier Shinzo Abe, who rose to political prominence campaigning for tough action against North Korea over the abductions.
Removal from the blacklist would open up impoverished North Korea to US aid and loans from international financial institutions.
Foreign Minister Masahiko Komura said that Japan accepted that the United States had made the delisting "a card" for progress in the denuclearisation deal.
"But at the same time we have been requesting to use their card to solve the abduction issue," Komura told a news conference.
"If the United States is going to delist North Korea as a terrorist country, then this should be used as an occasion to help resolve the abduction issue," Komura said.
He said he would talk Friday with US Secretary of State Condoleezza Rice, who is set to visit the western city of Kyoto for Group of Eight major industrial nations talks, about further action.
"The United States fully understands Japan's position, although maybe they fully understand it in their own way," Komura said. "We would like to have thorough talks with her and take whatever action is possible to tackle this issue."
Rice, who is starting her tour of Europe and Asia, vowed Monday to maintain pressure on North Korea over the abductions, saying Japan was "one of America's strongest allies."
"The United States will not set aside the abduction issue," Rice said.
North Korea admitted in 2002 to having kidnapped 13 Japanese citizens. It returned five victims and their families, and then said the case was closed.
But in an about-face, Pyongyang said earlier this month that it would reopen an investigation into the abduction victims, a move seen as tied to its desire to come off the terror list.
Japan in turn relaxed some sanctions on North Korea, although it continues to refuse to provide fuel aid as part of the six-nation disarmament deal.