The government secretly transferred the gang members March 8 to a jail with fewer restrictions.
In return, gang members committed themselves to stop ordering murders, but it was unclear how long the truce will last, Bishop Colindres said.
The agreement has been embroiled in controversy since the online newspaper El Faro reported March 14 that the government arranged the transfers in exchange for secret payments of cash to the gangs.
In an interview with Catholic News Service, Bishop Colindres denied any wrongdoing.
"I have asked on behalf of God for the human dignity of one of the most vulnerable groups of society, the inmates, and my request (to help them) was echoed," Bishop Colindres said.
"I never heard of money. If I had heard it, I would not have taken that step," he said.
"This is a pastoral initiative and, with the help of God, we hope to reach as far as possible," the bishop added.
El Salvador is one of the world's most violent countries, with an annual homicide rate of 70 per 100,000 people, according to international studies. Many of the killings are ordered by gang members from prison.
Bishop Colindres said inmates told him they are aware of the danger gang violence poses to Salvadoran society and that they are willing to ratchet down their actions in an effort to change the country's culture.
"Gang members have a historic opportunity to redeem themselves, to acknowledge their crimes and apologize to society," he said.
The administration of Salvadoran President Mauricio Funes, who has worked to change the international perception of the small Central American country, has denied negotiating with the gangs. The administration confirmed reports that the inmates were transferred because of the risk of a massive escape from the jail in Zacatecoluca.
Since the transfer of inmates, homicides have declined from an average of 14 murders daily to about five, according to law enforcement statistics.