Japan and the United States on Tuesday marked the 20th anniversary of an accord to relocate a major US military base on the southern Japanese island of Okinawa, amid persistent disagreement on where to move it.

The two countries agreed in 1996 to move the US Marine Corps Air Station Futenma, currently in Ginowan city, away from residential areas, and return the land to Japan, after the 1995 rape of a 12-year-old local schoolgirl by three US servicemen.

The work was to be completed within five to seven years, but has faced delays including fierce resistance from locals and conservationists over the suggested alternative site on a relatively unpopulated part of northern Okinawa.

On Monday, visiting US Secretary of State John Kerry and Japanese Foreign Minister Fumio Kishida reaffirmed the two countries' pledges to move forward with building a new base in Nago city for the Futenma troops.

US President Barack Obama reportedly voiced concerns about delays to the plan during his meeting with Japan's Prime Minister Shinzo Abe in Washington in late March.

"The Futenma base has not moved even one millimetre ever since," said Professor Akikazu Hashimoto, an expert on Japan-US relationship at JF Oberlin University in Tokyo.

"Japan has to ask itself where Japan's diplomatic problems lie," Hashimoto said. "The United States and Japan should really work hard and consider what kind of security relations they need to rebuild in East Asia, including Okinawa."

In the 2014 gubernatorial election on Okinawa, Takeshi Onaga, who vowed to oppose the new US base on the island, won a resounding victory over Tokyo-backed incumbent governor Hirokazu Nakaima.

In 2013, Nakaima approved a landfill project to create space for the base, reversing a 2010 election pledge to have the Futenma base moved entirely off the island, 1,600 kilometres south-west of Tokyo.

Many Okinawans have long been critical of the US military presence on the island and crimes committed by US troops. Older residents hold bitter memories of World War II as about 200,000 people, including 12,500 American soldiers, were killed during the Battle of Okinawa, one of the fiercest ground battles of the war.

Last month, a US serviceman was arrested for suspected raping of a Japanese woman visiting Okinawa at a hotel in the prefectural capital of Naha. He was indicted earlier this month.

"The direct link between the presence of US bases in Okinawa and humans rights violations in Okinawa has been made apparent time and again," the island’s Ryukyu Shimpo newspaper said in an editorial.

The United States has around 54,000 military personnel, 42,000 dependents, and 8,000 US civilian employees on bases in Japan, under a 1960 deal that followed the US occupation after World War II. Around 75 per cent of the US military facilities in Japan are on Okinawa.

On Sunday, about 200 islanders took to the streets, calling for the Futenma land to be returned to the locals as soon as possible.

Around 80 per cent of Okinawans have said they want the US military base off the island, according to polls.

Protester Tamayo Yamashiro was pregnant when the accord to relocate Futenma was first struck in 1996.

"I felt glad, as I thought the base would be gone by the time my child could walk and talk," she was quoted as saying by Kyodo News agency.

"But that feeling was replaced by anger after learning that the facility would be moved within the [Okinawa] prefecture.”

"Why do only Okinawa residents have to shoulder the burden of hosting the base?" she asked.

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