He studied under Edayoshi Shin’yo, a scholar of the Saga domain and elder brother of the statesman Soejima Taneomi, and in 1859 became an official in the service of the domain.
In 1862 he left Saga without receiving official permission and went to Kyoto, where he associated himself with the courtiers and joined the movement to restore power to the emperor and expel the foreigners. Later he was sentenced by the Saga authorities to be held in room confinement for an indefinite period. With the restoration of power of the emperor in 1868, he was pardoned and became a military official in the headquarters of the imperial army assigned to march on Edo. After the army reached Edo and took over control of Edo Castle, Eto played an important part in civil administration and also recommended that the capital be moved from Kyoto to Edo.
In 1869 he returned to Saga and devoted himself to carrying out reforms in the administration of the domain, but the same year he was ordered to return to the service of the central government, being assigned to an office in charge of institutional affairs. In company with Mori Arinori and Kanda Takahira, he helped to plan and set up deliberative organs and a legal system for the new government.
In 1871, after the old feudal domains were abolished and prefectures set up in their place, Eto served as vice-minister of education and vice president of the Sain, a legislative body. In 1872 he became minister of justice and, in connection with the establishment of a police system, was ordered to make a tour of Europe, but the plan never materialized, Kawaji Toshiyoshi being dispatched instead to inspect the police systems of various countries.
In 1873 he became a councilor of state and expressed sympathy with Saigo Takamori’s call for an expedition against Korea, but the plans for such an expedition were thwarted by opposition from Iwakura Tomomi and Okubo Toshimichi, who had just returned from their inspection tour of Europe, and Eto resigned his position as councilor. In 1874 he joined Itagaki Taisuke and others in petitioning the government for creation of an elected legislature. Around the same time, responding to invitations from those who favored an attack on Korea, he returned to Saga, where he became the leader of the disaffected samurai groups who opposed the policies of the government. In the same year, he joined with Shima Yoshitake and others in raising an armed rebellion in Saga, but it was quickly suppressed by government troops. Eto went into hiding, but was arrested in Kochi Prefecture. He was sent back to Saga, tried on the spot, and executed. In the general amnesty that accompanied the promulgation of the Meiji Constitution in 1880, he was posthumously cleared of the charges against him.