Hadnott was released Friday night after the girl withdrew her criminal complaint against him, according to Ryo Fukahori, a ministry official in charge of Japan-U.S. security. The district prosecutor's office in the prefectural capital of Naha then dropped charges against Hadnott. Rape charges in the Japanese judicial system can only be filed with a victim's complaint.
"The girl told us that she wished to be left alone," Chief District Prosecutor Yaichiro Yamashiki was quoted by Kyodo as telling reporters. "Considering her feelings, we decided that it was not appropriate to pursue our indictment."
Japanese Prime Minister Yasuo Fukuda and U.S. Ambassador Thomas Schieffer met after Hadnott's release.
"We are going to continue the investigation," Schieffer told reporters after the meeting. "We don't want these kind of incidents in the future."
A Marine was transferred to a Marine facility Friday evening and is under investigation, said Second Lt. Kurt Stahl of the U.S. Marine Corps on Okinawa. He said it was premature to speculate about possible judicial action.
Stahl declined to comment on the nature of the investigation and would only confirm that the transferred Marine was the one who has been accused of raping the teenage girl. The U.S. Marines would not release the name of any serviceman unless he was formally charged, Stahl said.
Another military official told the American military newspaper Stars and Stripes that Hadnott was being investigated in U.S. custody.
"Hadnott has been released by Japanese police and is now in U.S. military custody," Marine Master Sgt. Charles Albrecht, spokesman for Marine Corps Bases Japan, told the paper, in its online edition.
Japanese police earlier said Hadnott had admitted to investigators that he forced the girl down and kissed her but that he denied raping her.
Hadnott's Feb. 11 arrest and a series of other criminal accusations against some of the 50,000 American troops based in Japan have inflamed anger at the U.S. military presence.
Public broadcaster NHK said Okinawans would hold a protest meeting later this month.
In December, the U.S. military charged four servicemen in the rape of a 19-year-old woman in Hiroshima. Japanese prosecutors had dropped charges against the four, based in the U.S. Marine Corps Air Station in Iwakuni in southern Japan, citing lack of evidence.
The U.S. military has since imposed tight new restrictions on troops, their families and civilian expatriates in Okinawa and elsewhere, limiting them to bases, workplaces and off-base housing. The military held a "day of reflection" last week to urge troops not to commit crimes.
Japan also has introduced new security steps to curb crime around bases, including expanded information exchanges between the two countries as well as installation of surveillance cameras and joint patrols of entertainment districts around bases on Okinawa.