TOKYO - The governor of Okinawa Monday ordered a halt to construction of a controversial US military airbase, the latest twist in a saga that has riven southern Japan for decades.

Setting up a new clash between the central government in Tokyo and the independently minded semi-tropical island chain, Takeshi Onaga told a news conference he could revoke a drilling permit if the defence ministry does not comply with his order. Onaga, who opposed the airbase, was elected in November. His predecessor had agreed to the drilling needed in the sparsely populated coastal region to relocate Futenma airbase, which now sits in a crowded urban area.

"Because rock drilling has apparently been carried out (outside the area covered by the permit), I ordered them to suspend the work while the prefecture probes the issue," Onaga said.

Research by the Okinawa government last month found coral reefs in the area had been damaged by one of the concrete blocks sunk there as part of a survey.

In Tokyo, Chief Cabinet Secretary Yoshihide Suga described Onaga's move as "regrettable".

"The construction work is taking place after (Okinawa) agreed on it. It's impossible" that the work be suspended, he told reporters.

Defence minister Gen Nakatani was robust in his rejection of Onaga's move.

"We will continue the work without making a fuss... we don't think there was any wrongdoing," he said.

Around half of the 47,000 US servicemen stationed in Japan are based in Okinawa, a strategically vital archipelago.

While most Japanese value the protection the US military alliance gives them, especially in the context of China's growing assertiveness in regional disputes, many Okinawans want the Americans to leave the island chain.

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 allay local anger after the gang-rape of a schoolgirl by servicemen.

But it has been bogged down ever since, with local politicians blocking the move in an attempt to reduce the American footprint.

In 2013 Onaga's predecessor Hirokazu Nakaima agreed to drop his opposition to the new base in exchange for a hefty annual cash injection to the local economy.

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