Jose Guillermo Garcia, 82, was seen arriving at San Salvador's international airport with 131 other Salvadorans forcibly expelled from America yesterday, to cries of "murderer, murderer" from waiting rights activists.
The US embassy in El Salvador informed authorities that Garcia, a retired general who served as minister from 1979 to 1983, was deported after his application to stay in the United States was rejected by an immigration appeals court.
A US judge had signed his deportation order for his role "in the commission of human rights violations during El Salvador's civil war," it said.
A coordinator for El Salvador's Human Rights Commission, Miguel Montenegro, told AFP that Garcia was minister when a San Salvador archbishop, Oscar Romero, was murdered during mass in 1980, and when the Salvadoran army massacred 800 people in the village of El Mozote the following year.
"He would have much to confess in court," Montenegro said.
However that prospect is removed in El Salvador under a 1993 amnesty law pardoning those who committed rights crimes during the civil war.
Other retired Salvadoran military officers also went to America after the war.
A colonel who was minister for public security between 1989 and 1992, Inocente Orlando Montano, is in a US prison serving 21 years for migration fraud and perjury.
Spain is seeking his extradition on accusations of having participated in the murder of seven Salvadoran-Spanish Jesuit priests and two women in 1989.