The announcement adds a new twist to an investigation that has come under fire from international human rights groups and independent investigators.
The attorney general's office has charged municipal police officers in connection with the mass abduction in the southern city of Iguala on September 26-27, 2014.
But the governmental rights commission said that an eyewitness saw two federal agents near Iguala's courthouse, where municipal officers had stopped a bus carrying 15 to 20 students.
The commission also said another local police department, from the town of Huitzuco, had a previously unknown role in the disappearance.
The bus was one of five that around 100 students had seized that night in order to use them for a future protest.
Jose Larrieta Carrasco, a commission official investigating the Iguala case, said authorities should look into a "new route in the disappearance" of the students.
The attorney general's office declared last year that Iguala and Cocula police officers abducted the students and delivered them to a drug cartel.
The gang then killed the students, incinerated their bodies at a garbage dump in Cocula, and dropped the remains in a nearby river.
But experts from the Inter-American Commission on Human Rights who conducted an independent investigation said that there was no scientific evidence that the 43 students were incinerated at the dump.