In 1891, he refused to participate in naval actions against José Manuel Balmaceda's government in the 1891 Chilean Civil War and was separated from the navy.

Toro was deeply affected by the terrible living conditions of the islanders, who were suffering from the mistreatment of other expeditions searching for slaves and wealth.

After returning to Chile, he was promoted to 1st Lieutenant and awarded the position of Second Commander of the Magallanes Gunship due to his important work during the War of the Pacific.

Toro was appointed professor at the Naval School in 1883, promoted to Lieutenant Commander, and held administrative positions in the Chilean Navy three years later.

This prompted him to address a memoir to President José Manuel Balmaceda in order to convince him of the usefulness of taking possession of the island.

However, during the Chilean civil war in 1891, Toro remained loyal to President Balmaceda, leading to his arrest and subsequent release from the army.