President Obama’s visit to Japan got off to a rocky start on Wednesday when Japanese Prime Minister Shinzo Abe vented his anger over the alleged murder of a Japanese woman by an American civilian.

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During a joint press conference just hours after Obama landed in Japan, Abe said through a translator he expressed his “profound resentment” to the president about the “absolutely despicable crime” in Okinawa.

A Marine veteran working on a U.S. military base in Okinawa was arrested last week in connection with the killing.

The prime minister said he spent his entire meeting with Obama speaking about the incident.

The killing resurfaced longstanding irritation in Japan about the post-World War II U.S. military presence there. It also threatened to overshadow Obama’s agenda in Japan, which includes a meeting with leaders from Group of Seven world powers and a historic visit to the nuclear bombing site in Hiroshima.

Obama acknowledged that the killing “has shaken up people in Okinawa as well as people throughout Japan” and pledged that the U.S. would cooperate fully with the investigation.

The president said he "extended my sincerest condolences and deepest regrets" to Abe during their meeting.

“We consider it inexcusable and we are committed to doing everything that we can to prevent any crimes from taking place of this sort,” he said, adding that the status of forces agreement governing U.S. troops there does not prevent the prosecution of the suspect.

Residents in Okinawa have long complained about the U.S. military bases there, saying they bring crime and unwanted noise to the area.

The 1995 rape of a young Japanese student by a military service member sparked widespread demonstrations against the bases.

Abe said Okinawa residents once again have a “strong sense of uneasiness about their security” because of the latest incident.

The killing occurred at a time when both countries are trying to relocate a U.S. Marine base to a less-populous part of Okinawa island. Local opposition to the plan has been inflamed by the murder case.

Obama disputed Abe’s claim that the two only discussed the killing. He said they also discussed issues such as maritime security, trade, Middle East refugees and the Paris climate agreement.

Abe also said he "wholeheartedly" welcomes Obama's visit to Hiroshima, expressing hope it will renew focus on eliminating the world’s stockpile of nuclear weapons.

But he said he has no plans to reciprocate the president's visit with a trip to Pearl Harbor, where the Japanese carried out a surprise attack in 1941, drawing the U.S. into World War II.