Mr. Trump and his advisers are bogged down in difficult trade negotiations with China, and waiting on congressional Democrats — who are now preoccupied with an impeachment inquiry — to approve the revised North American Free Trade Agreement with Canada and Mexico. The Trump administration is also poised to levy new tariffs on billions of dollars of European products as part of a dispute over European aircraft subsidies, exacerbating trans-Atlantic trade tensions.

The Japan deal may help quiet criticism from American farmers who have complained of lost markets as a result of Mr. Trump’s trade war with China and his withdrawal from the Trans-Pacific Partnership, a multicountry trade deal that would have reduced trading barriers with Japan.

In a statement on Wednesday, the Office of the United States Trade Representative said that under the deal, American farmers and ranchers would have the same advantages in Japan as the countries that signed on to the Trans-Pacific Partnership without the United States.

But later in the day, Japanese officials said that while the pact was “within the scope” of Japan’s other trade deals it did not contain the same benefits the Trans-Pacific Partnership had offered for rice, fish or forestry products.

Atsuyuki Oike, a chief negotiator for the Japanese, also pushed back on reports this week that Japan had requested a provision that would cause the deal to expire if Mr. Trump imposed car tariffs on Japan, insisting that the potential tariffs were an important issue but not part of the trade text itself.

He said Japan was negotiating “on the assumption” that if the agreement was struck, the United States would not impose tariffs on Japanese cars, and that language was put into a joint statement from the countries to confirm that understanding.

Mr. Oike added that Japan had also confirmed that the United States would not restrict the quantity of Japanese car exports in the near future, and that the two sides would discuss a reduction in the United States’ 2.5 percent tariff on imported passenger cars in their next round of talks.