The suspect, a crew member on the USS Cowpens, is accused of stabbing 61-year-old taxi driver Masaaki Takahashi on March 19 in Yokosuka, just south of Tokyo and the site of a large US naval base.
Police also accuse him of failing to pay the 19,560 yen ($190) taxi fare.
The suspect confessed to the murder and police plan to send him to prosecutors on Saturday to be indicted, the spokesman said.
The suspect had been in US custody since navy authorities apprehended him in Tokyo on March 22 on an earlier desertion charge and was handed over to Japanese authorities under a bilateral security pact, Takashi Ariyoshi, a Japanese foreign ministry official, said.
US envoy summoned
Masahiko Komura, the Japanese foreign minister, summoned the US ambassador, Thomas Schieffer, on Thursday and urged US officials to step up anti-crime measures.
Schieffer also met Ryoichi Kabaya, Yokosuka's mayor, who said he was "enraged".
"We demand the US take concrete measures so that crimes like this are never repeated," he said.
Rear Admiral James Kelly, the top US naval commander in Japan, bowed and apologised to the mayor.
Schieffer called the killing "a shock and outrage to all those who believe in a civilised society".
"It puts a stain on all of us who try to serve America here in Japan," he said.
Nearly 50,000 US troops are stationed in Japan under the US-Japan security alliance, a pillar of Tokyo's diplomacy.
Last month, thousands of residents of the southern island of Okinawa rallied to protest against crimes by US troops and to demand a smaller US military presence in the prefecture, after a US marine was arrested on suspicion of raping a 14-year-old girl.
Japanese prosecutors dropped that case after the girl withdrew her complaints but the Marine was being investigated by US authorities for possible violations of the military code.
Four other US marines from a base in southwest Japan face court martial over the rape of a Japanese woman last year.
Tom Casey, the US state department deputy spokesman, said on Thursday that the US regretted these cases.
"There have been a number of individual incidents that have occurred involving US service members involved in criminal or other kinds of inappropriate activities and behaviours," Casey told reporters.
"And we deeply regret any of those actions," he said.
The US navy in Japan said on Wednesday it would ban until April 7 public drinking and the sale of alcohol at naval bases and restrict its personnel to bases from 10pm to 6am except for essential travel as part of a period of mourning for the murdered taxi driver.
Under an agreement on the status of US military personnel in Japan, members of the military suspected of crimes need not be handed over to Japanese authorities until they are charged.
But Washington has promised to favourably consider handing over suspects of crimes such as rape before indictment.
Japanese opposition parties and Okinawa politicians have demanded that the agreement be revised to give Japanese authorities greater legal jurisdiction.