Japanese Chief Cabinet Secretary Nobutaka Machimura said the protest called on Washington to take strong measures to prevent similar incidents in the future, the Kyodo news agency said.
Police arrested a 38-year-old U.S. Marine staff sergeant based at Camp Courtney in the rape which allegedly occurred Sunday. No charges have yet been filed, Kyodo said.
The suspect has denied the allegation. The United States is cooperating with Japanese authorities in the investigation.
Foreign Minister Masahiko Komura expressed concern over the incident's impact on an agreed plan to realign the U.S. military presence in Japan, including the relocation of the U.S. Marine Corps' Futemma Air Station, Kyodo said.
In parliament, Prime Minister Yasuo Fukuda was quoted as saying, "I'm taking it as a serious issue" and urged his Cabinet to "deal steadfastly" with it.
In Okinawa, a peace movement group held a protest meeting Tuesday in front of a U.S. military base.
The incident has revived memories of a 1995 rape of a 12-year-old schoolgirl by three U.S. servicemen, Kyodo said. That incident resulted in the decision to relocate the Futemma base and vacate some other facilities.[