The Trump administration has agreed to correct an “extremely regrettable” blunder in the execution of its trade agreement with Japan, the country’s top trade negotiator said in Washington on Thursday.

In negotiations last month, Japanese officials believed they had secured a deal that, in return for pledges to invest hundreds of billions of dollars in the United States and open its market to more American goods, would set a standard tariff rate of 15 percent for all of its products shipped to the United States.

In a July 31 executive order, the Trump administration outlined a similar scheme for the European Union. But Japan, along with other trade partners, was issued a new tariff rate that would be “stacked” on top of existing ones. In Japan’s case, that raised tariffs on items such as its beef exports to the United States from 26.4 percent to 41.4 percent.

Now, after Japan’s chief trade negotiator, Ryosei Akazawa, went to Washington this week for his ninth round of trade talks, Mr. Akazawa said he had secured a promise from the Trump administration to fix the error. Local media had earlier reported that the United States was not planning to revise the presidential order, citing unidentified White House officials.

This latest development is another example of how a deal with no publicly disclosed written joint agreement — assembled quickly just days before higher threatened tariffs were set to take effect — is causing confusion and growing tension between the United States and one of its top allies and trading partners.