Fr Antonio Rodriguez Tercero had been released on bail on Monday but was immediately rearrested accused of trying to move gang members to more open jails and asking officials to stop blocking mobile phone signals behind bars.
It's claimed there are phone recordings in which the priest is heard asking for signals to be allowed in the prison.
He's also accused of negotiating the transfer of several gang members to more lenient jails in the country.
Supporters of the priest have held protests about the charges outside the court where his case will be held.
Fr Tercero is a fierce critic of El Salvador government's policy on gangs and reportedly claims he's been targeted because of his 'honesty'.