Defense Secretary Ash Carter spoke by phone Saturday with his Japanese counterpart after an American who works on a US air base in Okinawa was arrested for his links to the death of a local woman.
In the call to Gen Nakatani, Carter "conveyed his sadness and his regret" over the murder of the young woman "and extended his sincere apologies to the victim's family and friends," the Pentagon said in a statement.
Okinawan police arrested Kenneth Franklin Shinzato on Thursday for allegedly disposing of the woman's body in a weed-covered area in southern Okinawa.
Shinzato, a US citizen and former US Marine who works at the Kadena Air Base, has reportedly admitted to raping and killing 20-year-old Rina Shimabukuro, who had been missing since late April.
Nakatani on Saturday traveled to Okinawa to lodge a formal protest with the US base commander.
"I deliver a strong message of regret and at the same time make a protest," Nakatani told US military commander Lieutenant General Lawrence Nicholson, according to Japanese public broadcaster NHK, as he demanded that the US military in Okinawa ensure discipline among troops.
In the phone call, Carter told Nakatani "that the United States hopes the perpetrator of this crime will be held accountable under the Japanese legal system."
Carter also said the military "is determined to cooperate fully" with the Japanese authorities to investigate the case.
The statement described the murder as a "shocking and tragic incident."
The statement was released as President Barack Obama departed Saturday on a trip to Vietnam and Japan that will include the first visit by a sitting US president to Hiroshima, site of the world's first nuclear attack.
The southern island of Okinawa was the site of a brutal World War II battle but is now considered a strategic linchpin by hosting numerous US military bases that support the two countries' decades-long security alliance.