Prosecutors accuse the former president, who governed the Central American country between 1989 and 1994, of first failing to stop, then helping to cover up the murder by soldiers of the priests, their housekeeper and her daughter at the campus of the Central American University in the early hours of Nov. 16, 1989.

The arrest order means Cristiani could be held for at least three months, the court in San Salvador said.

Cristiani dismissed the charge in a letter published on Twitter by his daughter Claudia.

"The attorney general, in bad faith and with clear disregard for the truth, has publicly accused me of doing nothing and a cover-up. The truth is that I never knew of the plans they had to commit those murders," Cristiani wrote in the letter.

The murder of the priests, five of whom were Spanish, and the two women is one of the most notorious atrocities in El Salvador's civil war. Several high-ranking and retired soldiers are currently being tried over the case by the court.

The 1980-1992 civil war between El Salvador's U.S.-backed army and Marxist guerrillas left some 75,000 dead and 8,000 missing.