Tariffs on frozen beef will jump to 50 percent from the current 38.5 percent between Aug. 1 and the end of March next year, as a "safeguard" mechanism to protect domestic farmers is being triggered, the ministry said in a statement.
The increase will be the first time the tariff mechanism has been tripped for beef imports since it was last triggered for chilled beef in August 2003, the farm ministry said.
The increase threatens a significant sector of United States' access to the biggest Asian market for U.S. beef overall, just as President Donald Trump is trying to expand American exports to Japan.
A tariff increase is automatic if quarterly imports for specific types of beef products - both from all nations and from those that do not have economic partnership agreements (EPAs) with Japan - rise more than 17 percent from a year earlier.
In April-June, Japan's first fiscal quarter, frozen beef imports from all nations totalled 89,253 tonnes, up 17.1 percent from a year ago, and imports from non-EPA nations reached 37,823 tonnes, up nearly 25 percent, government data showed.
Nations that have EPAs with Japan, such as Australia, Mexico and Chile, will be excluded from the hike in tariffs. Japanese Finance Minister Taro Aso told reporters the government has been contacting affected nations such as the United States to explain the increase, Kyodo news agency said.