The Japan Medical Association on Saturday elected Vice President Toshio Nakagawa as president, replacing Yoshitake Yokokura, who was close to the Abe administration.
The leadership change may affect that relationship, observers said. The JMA is a key supporter of Prime Minister Shinzo Abe's ruling Liberal Democratic Party.
Yokokura, 75, helped the JMA coordinate with the government on coronavirus measures and talks to revise medical fees.
In the election, Nakagawa, 69, received 191 votes to Yokokura's 174 , denying Yokokura a fifth two-year term. Nakagawa, who became vice president in 2010, began his first term the same day.
Yokokura initially planned to step down but later changed course, saying he was strongly asked by many people to change his mind and stay.