The "provisional detention" of Cristiani, whose whereabouts are unknown, stems from an amnesty he declared after the 1981 killings as part of a "personal cover-up," according to a court resolution confirmed to AFP by Alejandro Diaz, a lawyer for victims' relatives.
The order, which also calls for the arrest of four Cristiani deputies, was issued by a court in the city of San Francisco Gotera, which is prosecuting several members of the Salvadoran military for the massacre.
Considered the largest in Latin America, the Mozote slaughter was perpetrated during the country's 1980-1992 civil war.
"We are interested in seeing that all those responsible be prosecuted," including those who hindered investigators, Diaz said.
According to the resolution, Cristiani and the others covered for those responsible by promoting a law -- passed in 1993 but revoked in 2016 -- that guaranteed "absolute impunity" to the authors of the massacres.
- Priests killed -
In 2012, the Inter-American Court of Human Rights condemned the Salvadoran state for its role in the killings.
From December 9 to 13, 1981, Salvadoran army units -- led by the US-trained Atlacatl counterinsurgency battalion -- launched an operation in Morazan department.
The government determined in 2017 that at least 988 people, including 558 children, were murdered in and near El Mozote for allegedly supporting the leftist rebels of the Farabundo Marti National Liberation Front.
Overall, the Salvadoran conflict left more than 75,000 people dead and at least 7,000 missing.
In March 2022, another judge ordered Cristiani's arrest for allegedly taking part in planning the assassination of six Catholic priests and two others.
Cristiani has denied all charges.
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