Finance Minister Taro Aso announced the move Friday, saying he was prepared to explain the decision to the US side.
Japanese officials said on Friday they were raising duties on US frozen beef exports to 50% from 38.5%. Under World Trade Organization rules, Japan can introduce safeguard tariffs when imports rise more than 17% year-on-year in any given quarter.
The increase threatens a significant sector of the United States' access to the biggest Asian market for USA beef overall, just as President Donald Trump is trying to expand American exports to Japan.
The expected ample USA beef supplies could mean export prices fall to compensate for the increased tariffs or demand could switch to chilled beef imports.
Japan has made a decision to impose emergency tariffs after frozen beef imports reached 89,253 tonnes in the April-to-June quarter, up 17.1 per cent from a year earlier.
National Cattlemen's Beef Association (NCBA) president Craig Uden expressed disappointment in the tariff increase and encouraged USA government officials to pursue a bilateral agreement with Japan.
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"It will be especially hard for the gyudon beef bowl restaurants that rely heavily" on US beef, the statement said.
The move, the first such step in 14 years involving beef, comes after President Donald Trump named Japan as one of the countries contributing to the USA trade deficit.
USA farmers had been hoping for wider access to Japan's lucrative market through a Pacific Rim trade initiative, the Trans-Pacific Partnership.
Tyson Foods Inc, the largest meat processor in the United States, said on Friday it supported US government efforts to address the issue with Japan.
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 US and Australia account for 90 per cent of all imports of frozen beef, which is mostly used by beef bowl, hamburger and other fast food outlets.
USMEF explained that the snapback duty of 50% will apply to frozen imports from suppliers that do not have an economic partnership agreement (EPA) with Japan, which are mainly the U.S., Canada and New Zealand.