The event rocked the government, which says the students were abducted by corrupt police in the southwestern city of Iguala on the night of Sept. 26, then probably incinerated by members of local drug gang Guerreros Unidos.
The remains of only one of the 43 students have been identified, and the government blames former Iguala mayor Jose Luis Abarca and his wife Maria de los Angeles Pineda for masterminding their disappearance, along with the gang.
Later on Monday, security forces in Iguala clashed with students from the same teacher training college and other protesters trying to break into a local military base, a police spokesman said. Four people were injured, media reports said.
The courts authority said it believed Pineda had been working with Guerreros Unidos since at least 2005, and accused her of engaging in crimes against health, which includes drug trafficking, and managing illicit funds.
Her lawyers could not immediately be reached for comment.
The statement made no specific reference to Iguala.
President Enrique Pena Nieto is facing his deepest crisis over the government's handling of the investigation.
A federal judge found evidence that Pineda acted as a financial intermediary for Guerreros Unidos and helped protect the gang, the courts authority said.
Between 2009 and 2014, she took deposits probably originating with the drug gang worth about 13.7 million pesos ($936,016) in four bank accounts, the court said.
Pineda and Abarca fled Iguala a few days after the abduction of the students, and were captured in November by police.