Secretary of State Condoleezza Rice in her attempt to ask Japan’s help in urging North Korea to drop the nuclear weapon plans, said on Wednesday that she hopes the incident of the alleged rape won’t harm U.S.-Japan ties.

After her trip to China, where she left behind her aides, Rice came to Japan in order to tamper the outrage triggered by the incident which occurred earlier this month.

She said: "We certainly hope that there will not be lasting effects, it's a long-standing and strong alliance. Our concern right now is to see that justice is done, to get to the bottom of it and our concern is for the girl and her family. We really, really deeply regret it," the Associated Press reports.

A Marine was arrested on suspicion of raping a 14-year-old Japanese girl on the island earlier this month while some of the 50,000 American troops were accused of other criminal acts. These incidents brought upon the U.S. military presence Japan’s anger.

Rice held talks with Japanese officials, including Prime Minister Yasuo Fukuda, Foreign Minister Masahiko Koumura and Defense Minister Shigeru Ishiba and said that measures will be taken in order to prevent future incidents.

At a news conference, Koumura said: "Although we have these problems ... Japan-U.S. security cooperation has continued to progress in a positive direction and I agreed with Secretary Rice that further progressing these relations would be in the interests of both Japan and the United States."

The incident occurred just as six countries, including Japan, are involved in a plan to make North Korea get rid of its nuclear weapons programs.

Tokyo was Rice’s third stop in her Asian tour on this matter after she traveled to South Korea and to China where she held talks about how to make things happen faster.

China assured her that it will use its influence with North Korea.

She told Assistant Secretary of State Christopher Hill not to accompany her to Tokyo and to remain in Beijing to study on the ideas she and Chinese President Hu Jintao came with.

Rice said: "I thought it was worthwhile for him to continue those discussions and we have had constructive discussions here today and those will add to our ability to perhaps build some momentum."