After a 16-year legal battle, a former defense minister of El Salvador once embraced by Washington as a close ally during the civil war there in the 1980s, was deported on Wednesday after immigration courts found that he had participated in torture and killings by troops under his command.

The officer, Gen. Carlos Eugenio Vides Casanova, is the highest-ranking foreign official to be deported under laws enacted in 2004 to prevent human rights violators from seeking haven in this country. The expulsion culminates persistent efforts by rights advocates to hold General Vides accountable for his role in the 1980 murders of four American churchwomen, one of the most notorious crimes by the Salvadoran armed forces in that era.

General Vides landed at the international airport in Comalapa, El Salvador just after 12:30 p.m., one of dozens of Salvadoran deportees aboard an Immigration and Customs Enforcement charter flight, according to Mauricio Silva, a spokesman for the Salvadoran immigration agency. The general had been detained by immigration authorities in the United States since March 25.

The deportation “sends an enormously important message to El Salvador and the rest of the world that we are not going to harbor people who committed these violations even when at the time they appeared to be supporting U.S. policy,” said R. Scott Greathead, a lawyer who represented William Ford, the brother of Sister Ita Ford, one of the murdered churchwomen. Mr. Ford died in 2008.