Following the scandal-prone Yukon Gold Rush era administration of Thomas J. Humes, Ballinger was elected as Seattle mayor in 1904 and, with the support of the downtown business elite, he cracked down somewhat (but not heavily) on vice, opposed labor unions, and was a roadblock to the city's strong municipal ownership movement.
After serving as mayor of Seattle, Ballinger served as commissioner of the General Land Office from 1907–1908. In 1909, President William Howard Taft appointed him Secretary of the Interior. While Secretary, he was accused of having interfered with investigation into the legality of certain private coal-land claims in Alaska. After a series of articles in Collier's Weekly that roused the conservationists, an investigation was demanded. A congressional committee exonerated Ballinger, but the questioning by committee counsel member Louis D. Brandeis made Ballinger's anti-conservationism clear. He resigned in March, 1911. The incident split the Republican Party and helped turn the election of 1912 against Taft.