Obama expressed his "sincerest condolences and deepest regrets," adding that the United States will continue to cooperate fully and will continue to ensure "justice is done under the Japanese legal system."
"We want to see a crime like this prosecuted here in the same way that we would feel horrified and want to provide a sense of justice to a victim's family back in the U.S.," Obama said. "I think the Japanese people should know we are deeply moved and working with he Japanese government to prosecute not only this crime but prevent these kinds of crimes from happening again."
On Saturday, Secretary of Defense Ashton Carter apologized and offered condolences after the Okinawa woman was allegedly killed by U.S. Marine Kenneth Franklin Shinzato, a U.S. contractor working at the U.S. Kadena Air Base in Okinawa Prefecture who previously served as a Marine.
The incident inflamed the already tense feelings many Okinawans have toward the heavy U.S. military presence on the island.
The incident, which has garnered mass media attention in Japan, occurred Thursday when police said Shinzato, 32, abducted the woman near her apartment. Police said Shinzato confessed to raping Rina Shimabukuro, 20, then strangling and stabbing her and stuffing her body in a suitcase.
Shinzato has been charged with illegally dumping a body, a common first step in Japanese homicide investigations. Under Japanese law, suspects can be held for weeks before the formal charges are filed.
Eric DuVall contributed to this report.