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The tax increase, to be effective from January 1, is part of an adjustment to a tariff policy in 2011 that covered a wide range of imports and exports, the finance ministry said in a statement.
The ministry did not specify which rare earths would be affected or the size of the increase.
China has a near monopoly in rare earths — last year, it produced 97 percent of world supply.
The government has moved to tighten export controls on the elements, which are key components in products ranging from iPods to cars, citing pollution concerns. But the curbs have prompted complaints from foreign high-tech producers.
The commerce ministry said it had recently toughened rare earth export rules to allow only producers that meet environmental protection laws and international standards to sell the precious elements to overseas buyers.
Japan has depended on China for more than 90 percent of its rare earths supply, leaving its high-tech industry vulnerable.
Tokyo complained in the autumn that China had frozen its rare earth shipments amid a territorial row surrounding the arrest of a Chinese trawler captain whose boat collided with a Japanese patrol near a disputed island chain in September.
Japanese companies said rare earth shipments only resumed around the middle of last month, but Beijing denies they ever stopped.
Japanese companies have announced deals with Indian and Australian partners to diversify their rare earth supply sources away from dependence on China.
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