Leaders of the Mara Salvatruchas gang and the Mara 18 gang, who between them represent more than 100,000 members, have announced a truce by the church.
The head of the army and police chaplain Monsignor Fabio Colindres, who acted as an intermediary, have confirmed the peace agreement.
Church leaders have said they acted without government involvement, but some are questioning that explanation.
One gang leader told Al Jazeera that any truce agreement would be highly unlikely without the government taking part.
One investigative newspaper, El Far, also accused the government with involvement in the deal, claiming it had handed out concessions, including the transfer of 30 gang leaders to lower security prisons.
Al Jazeera's Rachel Levin reports.