The man, identified by Okinawan police as 24-year old Navy sailor Justin Castellanos, stationed at Camp Schwab in Okinawa, allegedly took the victim, a 40-year-old woman from the Japanese prefecture of Kyushu, to his room after finding her asleep, drunk, in the hotel's lobby before raping her.

Reports say that he has denied the accusation. The U.S. Embassy in Tokyo declined to comment on the incident.

Protests

On Thursday, police said they arrested a 52-year-old man, on suspicion of obstructing the performance of official duties around 9 AM local time (8 PM ET) in front of the gate at Camp Schwab in Henoko, Okinawa.

A man struck a policeman on the head with a protest sign during a demonstration against the construction of new U.S. base.

Apologies

The head of U.S. Marines in Japan, Lt. Gen. Lawrence Nicholson visited Okinawa Governor Takeshi Onaga, to apologize Wednesday.

"The allegations against this individual bring great shame and dishonor on all of us," he told the governor. "Never again will we have an incident like this again. You have my word that we will do everything we can."

Onaga responded: "I hear assurances of 'good neighbors' every time your office changes personnel, but it is my honest feeling that it has never been executed," according to a translation.

A U.S. State Department said in a briefing earlier in the week that the U.S. government takes "the reports very, very seriously," and said that the U.S. Navy was also investigating the incident.

"If there is a need to hold someone accountable, they will do that... (the Japanese government and U.S. Navy) will do that in open and transparent way," U.S. State Department spokesman John Kirby said.

"We take our relationship with the people of Okinawa as with everybody in Japan very, very seriously, It's a strong alliance, it's a deep and abiding friendship and we have great respect for the Japanese people.. If (the incident did occur), it's obviously inconsistent with our values and principles and what we expect of our people overseas."

Previous crimes

U.S. troops stationed in the prefecture have previously been convicted of assault and other crimes. In 1995, three U.S. servicemen, Rodrico Harp, Kendrick Ledet and Marcus Gill, who were at the time stationed in Okinawa, were convicted of the abduction and rape of a 12-year-old girl, and in 2013, two American sailors were convicted by a Japanese court of the 2012 rape of a Japanese woman that they were found to have followed from a bar.

In the past, crimes committed by U.S. troops have sparked huge protests in Okinawa and elsewhere in Japan. The bulk of U.S. forces in Japan are stationed in Okinawa and locals complain that they are shouldering an unfair burden.

This latest incident comes as Tokyo and the U.S. military have been attempting to relocate U.S. forces within Okinawa, mostly from the Futenma air base, which is located in an urban area, to a replacement base in the Henoko coastal area of Okinawa.

The Okinawa government recently won a court case with Tokyo over the creation of an alternate base at Henoko, although construction of a new facility has been ordered to continue at the site.

The case may affect the presence of U.S. troops in the southern prefecture, with a transfer of U.S. Marines from the southern prefecture to the U.S. Pacific territory of Guam, part of a wider realignment of U.S. forces in the Asia-Pacific region.