Trade minister Akihiro Ohata said that Zhang Ping, chairman of China's National Development and Reform Commission, told him that he had "instructed (officials) to speed up inspections at customs to be more efficient".
Ohata was briefing reporters on the sidelines of a summit of the Asia Pacific Economic Cooperation group of nations in Yokohama, Japan.
Zhang had told Ohata that China's "tightening of control over the rare earth industry is aimed at the orderly development and sustainable use of rare earth resources," the Japanese trade minister said.
"But he understands that Japan has interest in the freight stuck at customs, and that the NDRC has already contacted relevant organisations," said Ohata, adding that the issue of restricted shipments will be resolved soon.
Rare earth minerals are used in everything from guided missiles to iPods and cars, and Japan's high-tech industry is their largest user in the world.
China has a near-global monopoly on rare earths -- last year, it produced 97 per cent of world supply. It has denied any embargo on shipments, including to Japan, amid a diplomatic row between the Asian neighbours.
Since 2006, China has cut export quotas on rare earths by five to 10 per cent a year. Production has also been slashed amid concerns that Chinese supplies could run out in 15 years.
Ohata's comments suggested a more conciliatory tone on the issue, after Tokyo in recent weeks accused Beijing of limiting shipments in the wake of a simmering territorial row, which Beijing denied.
"We have to understand that China has provided about 97 per cent of rare earth materials to the world even though it has only one third of the (global) reserve, and maybe in ten to fifteen years it will dry up," Ohata said.
Tokyo's row with Beijing stems from the arrest of a Chinese trawler captain whose vessel collided with Japanese patrol boats in waters near a disputed island chain in the East China Sea in September.
Prosecutors released the captain after Beijing cut political, economic and cultural exchanges, but the dispute continued to simmer and nationalists in both countries have staged protests.
China's moves to restrict exports have spurred other countries such as the United States and Australia -- which have 15 and five per cent of reserves respectively -- to resume production.
On Friday China said it had toughened rare earth export rules to allow only producers that meet environmental protection laws and international standards to ship the precious elements out of the country.
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