In a statement, the Federal Judiciary Council said the prosecution would proceed against seven originally arrested in relation to Guzman's July 11 escape from a maximum-security prison.
It said prosecutors showed there was sufficient evidence that the employees assisted Guzman's escape through a 1.6km-long tunnel.
It described the employees as the person in charge of the prison's video surveillance control centre and two guards.
There were inconsistencies in the supervisor's statements and there was no explanation for why the guards did not answer the telephone in their module.
The Council also said that, at least for now, it was determined there was no cause to hold for prosecution the other four people detained in connection with the escape.
