Chief Cabinet Secretary Yoshihide Suga told reporters on Friday that Toyota was an "important corporate citizen," while Trade Minister Hiroshige Seko stressed the contribution of Japanese companies to U.S. employment.
"We think the impact on business performance is limited," Akira Kishimoto, a senior analyst at JP Morgan, said in a note.
"A cool judgement is needed."
Toyota's exposure to Mexico is limited, Kishimoto said, adding that even an "extreme case" tariff of 20 percent would hit its operating profit by around 6 percent. Trump has threatened a 35 percent tariff on cars imported from Mexico.
Toyota is just one of a host of companies operating in Mexico. It has an assembly plant in Baja California, where it produces the Tacoma pick-up truck, and where it could increase production.
Trump's tweet, however, confused Toyota's existing Baja plant with the planned $1 billion plant in Guanajuato, where construction got under way in November, days after the election.
The Guanajuato plant will build Corollas and have an annual capacity of 200,000 when it comes online in 2019, shifting production of the small car from Canada.
Baja produces around 100,000 pickup trucks and truck beds annually. Toyota said in September it would increase output of pick-up trucks by more than 60,000 units annually.
Other Japanese automakers and suppliers in Mexico include Nissan, which has been in Mexico for decades after choosing it as the site for its first assembly plant outside Asia. Nissan has two facilities there, producing 830,000 units in the year to March 2016.
Honda operates two assembly and engine plants with a total annual capacity of 263,000 vehicles, and a transmission plant with an annual capacity of 350,000 units.
Toyota suppliers Aisin Seiki Co. and Denso Corp. have two and three plants, respectively, in Mexico. Parts makers tend to cluster near assembly plants under the industry's "just-in-time" production practice.
