Shinzo Abe's right-hand man and the governor of Okinawa remained apart in a lingering row over the construction of a US air base at a meeting Sunday ahead of the Japanese premier's visit to Washington later this month.

The base's construction, first mooted in 1996, has been stymied by local opposition from islanders who say they bear a disproportionate burden in hosting more than half of the 47,000 US service personnel stationed in Japan.

In the latest twist in the two-decade row, Chief Cabinet Secretary Yoshihide Suga told Governor Takeshi Onaga: "We hope to get your understanding on the plan... for maintaining the deterrent power of the Japan-US alliance."

However, the Okinawan governor countered that while he understood the importance of the alliance with the US, any national security plan must have the Japanese people's support.

"Okinawa never voluntarily offered (land) for bases. I'm convinced that it is impossible to construct a new base", Onaga said, referring to a plan to replace the urban Futenma Air Base with one on a rural coastline at Nago.

After the meeting, he told reporters: "I will never step back on the base issue," criticising the government's top-down approach.

Hundreds of anti-base protesters rallied outside the hotel in Okinawa's capital Naha where the talks took place, holding banners that read "rescind the relocation plan!"

The anti-base camp -- who want the base off Okinawa -- struck a blow late last month when Onaga said coral just outside the permitted zone at the site on the island's northeast coast had been damaged and demanded a halt to the work.

The central government last week muscled the governor out of the way, suspending his stop-work order, and ahead of Abe's week-long US tour starting on April 26, which will focus on deepening trade and military ties.

The prime minister will meet US President Barack Obama on April 28 during the trip which ends May 3.

Abe and Onaga will meet before the US tour, the Mainichi Shinbun reported, citing unnamed sources from the Okinawa government.

- Base construction to continue -

Fisheries minister Yoshimasa Hayashi on Monday defanged the stop-work order with a suspension while the issue is probed, effectively kicking it into the long grass.

Suga later told reporters that Sunday's meeting "was the first step for talks between the government and Okinawa," but added the government will continue work on construction of the base.

The once-independent kingdom of Okinawa was annexed by Japan in the 19th century and was under US control from the end of World War II in 1945 until 1972.

While most Japanese value the protection the US alliance gives them, especially in the context of Beijing's growing regional assertiveness, a sizable proportion of Okinawans want a dramatic reduction in their numbers.

The shuttering of Futenma and the opening of a replacement base at Nago, 50 kilometres (30 miles) away, was first agreed in 1996 as the US sought to soothe local anger after the gang-rape of a schoolgirl by servicemen.

But it has been stymied ever since, with local protesters blocking the move, arguing any new base should be built elsewhere in Japan or abroad.

In 2013 Onaga's predecessor Hirokazu Nakaima, formerly a staunch opponent, dropped his objection to the new base after Tokyo promised a hefty annual cash injection to the local economy.

Many islanders saw this as a betrayal and in November kicked him out of office in favour of Onaga.

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April