And on a key national security matter, Japanese ministers, like those in Europe, have also expressed uncertainty about Bush's desire to establish a nuclear missile defense system.
While officially neutral on the matter, some officials are wary of the political bind they might find themselves in if the Bush administration asks them to take a more active role in developing the system. Such participation could be expensive and might threaten the anti-war foundation of the Japanese constitution.
Article II of the constitution, written by the United States after World War II, states "the Japanese people forever renounce war as a sovereign right of the nation and the threat or use of force as means of settling international disputes."
At a press briefing this afternoon, state department spokesman Richard Boucher said President Bush already "had been looking forward" to meeting with Mori, although no date has yet been announced for a conference between the two leaders.
Boucher also said the incident should not "detract from the overall positive nature of the U.S.-Japan relationship and the importance, I think, for both of us of pursuing that relationship."
Apologies and Condolences
The collision and sinking occurred Friday, several miles from the Hawaii island of Oahu, when the USS Greeneville was practicing an emergency surfacing operation.
The Japanese boat had 35 people on board, 26 of whom scrambled into three life rafts. Rescue crews have been searching for the other nine people, but with little hope finding them.
In the aftermath of the event, President Bush and Secretary of State Colin Powell both issued apologies and sent their condolences to Japanese leaders.
"We hope there won't be a negative effect in our relationship with Japan as a result of the accident," Powell said on Sunday. "We have expressed our apologies at every level, from the president through me, through the secretary of defense, through our military commanders."
But on Sunday, Mori lodged a protest with the United States, and has demanded that the ship be raised.
According to the Associated Press, Kazuhiko Koshikawa, Mori's spokesman, said the prime minister met with U.S. Ambassador Thomas Foley on Sunday and asked the United States to use "all available means" to salvage the 499-ton fishing boat.
In the meantime, U.S. leaders are expressing concern, trying to learn how the accident happened, and assuring their Japanese counterparts that the follow-up to the accident will be thorough.
"The United States government has brought the families over, and it's been putting people up and taking care of the situation," said Defense Secretary Donald Rumsfeld on ABCNEWS' This Week on Sunday. "And certainly it will do the proper thing when the facts are fully sorted out."
ABCNEWS' John McWethy contributed to this report.