Japan's prime minister publicly shamed President Barack Obama over a 'despicable' murder, allegedly at the hands of a former US Marine on Okinawa.

Obama sought to ease Japanese anger over the death of the woman by expressing his 'deepest regrets' and vowing the US would cooperate with them to prosecute Kenneth Shinzato, the American man arrested for the crime.

At a press conference with Obama, Prime minister Shinzo Abe publicly expressed his indignation over the case of Rina Shimabukuro, 20, who has been missing since late April and was reportedly raped and murdered.

'As Japanese prime minister, I protested sternly to President Obama over the recent incident in Okinawa,' Abe told reporters on Wednesday.

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Japanese Prime Minister Shinzo Abe (right) slammed President Barack Obama (left) over a 'despicable' murder allegedly at the hands of a former US Marine on Okinawa during a press conference in Shima, Japan, on Wednesday

Kenneth Shinzato (left, being taken from the police station in Uruma, Okinawa, and right) was arrested in connection with the missing woman's death

'I feel profound resentment against this self-centred and absolutely despicable crime,' Abe said on Wednesday.

Obama arrived earlier Wednesday for a two-day summit of Group of Seven countries, which formally begins Thursday.

'I extended my sincerest condolences and deepest regrets,' Obama added.

'The United States will continue to cooperate fully with the investigation and ensure that justice is done under the Japanese legal system.'

A series of crimes, including rapes, assaults and hit-and-run vehicle accidents by US military personnel, dependents and civilians have for years sparked local protests on the crowded island that hosts numerous US military bases.

Rina Shimabukuro (pictured) disappeared on the island of Okinawa, Japan, on April 28. Her body was found when Kenneth Shinzato, 32, a civilian worker at Kadena Air Base, gave police a location

But public anger boiled over last week after police arrested Shinzato, 32, in connection with the missing woman's death.

Shinzato, a US citizen who was working at the sprawling Kadena Air Base on Okinawa, was arrested for allegedly disposing of the woman's body, Okinawan police have said.

He has reportedly admitted to raping and killing Rina Shimabukuro, who had been missing since late April.

Obama sought to ease Japanese anger over the death of the woman by expressing his 'deep regrets' and saying the United States would co-operate in the prosecution of the American man arrested for the crime.

Obama is greeted by U.S. Ambassador to Japan Caroline Kennedy and her husband Edwin Arthur Schlossberg after he arrives at Chubu Centrair International Airport in Tokoname, Japan on Wednesday

Police suspect Shinzato was responsible for the woman's death but he hasn't formally been charged with the crime.

Shimabukuro was last heard of at 8pm on April 28, when she messaged her boyfriend to say she was going for a walk.

Shinzato was arrested after investigators found her body at a location he provided.

The case has threatened to overshadow a planned visit to Hiroshima immediately after the summit ends on Friday, though remarks by the two leaders likely helped clear the air.

Obama will become the only sitting US president to visit Hiroshima.

The visit to the world's first atomic-bombed city by Obama, who has a record of calling for global denuclearisation, has been well received in Japan.

Protesters hold a banner before US Kadena Air Base in Kadena, Okinawa, on Friday after Shinzato's arrest

Former US Marine Kenneth Shinzato is escorted by police officers from Uruma police station on May 20

But the heavy US military presence on Okinawa has long been a thorn in the side of the two countries' relations.

Abe on Monday told Okinawa's governor Takeshi Onaga that he would ask Obama to take action over crimes by US personnel on the southern island.

Okinawa was the site of a fierce World War II battle between the US and Japan but is now a key strategic outpost supporting their security alliance.

It hosts the lion's share of US bases in Japan and more than half the 47,000 American military personnel in the country under a decades-long security alliance.