The court ruled General Prosecutor Luis Martinez had to reopen a previous investigation that had fizzled out without any charges being filed. The court demanded prosecutors charge any guilty parties and release publicly the results of its probe.
The ruling is an unprecedented move by the court to order the probe into a particular case relating to the country's 1980-1992 civil war.
The Supreme Court said that the prosecutor's office dragged its feet in the original investigation and the justices ruled that the prosecutor had violated the rights of a group of citizens who had been filing legal complaints about the massacre since 2006.
Military troops allegedly killed about 45 people, including women and children, in the community of San Francisco Angulo.
"The court orders the General Prosecutor to carry out a serious, far-reaching, diligent and conclusive investigation, within a reasonable time," the court said in a statement.At the same time, the Constitutional Chamber of the Court has before it a proceeding challenging the general amnesty law passed in 1993 which has prevented the prosecution of this and other war crimes. In the upcoming presidential election, ARENA opposes any repeal of the amnesty law. Salvador Sanchez Ceren of the FMLN has waffled on the issue, once saying that he supported a repeal and later stating that repeal was up to the courts.