MEXICO CITY — A federal court in Mexico ordered the government on Monday to investigate the 2014 disappearances of 43 college students again, but this time under the supervision of a truth commission to be led by the nation’s top human rights body and parents of the victims.

The order came in response to legal motions filed by several defendants accused of taking part in the students’ violent abduction, which took place in September 2014 and quickly became an international scandal for the government of President Enrique Peña Nieto. The suspects accused the government of using torture to force confessions, an accusation that the United Nations also made in a recent report.

But rather than simply validate the allegations of torture, the three judges of the First Collegiate Tribunal of the 19th Circuit unanimously delivered a broad and sweeping indictment of the entire case, describing it as “neither prompt, effective, independent nor impartial.”

They accused the nation’s attorney general’s office of ignoring lines of evidence that contradicted its theory of the case, and they ordered the creation of a so-called truth commission to oversee the new investigation.