Christian Solidarity Worldwide is praising an agreement that also sets in place a plan for the demobilisation of members of the FARC, the country's largest illegal armed group.
In the past agreements have been made including provisions that those responsible for human rights violations fully confess to those acts in order to benefit from the possibility of reduced sentences.
Open Doors ranks Colombia on the list of worst places in the world to believe.
Leader: President Juan Manuel Santos
Population: 48.7 million, 46 million Christians
Main Religion: Roman Catholicism
World Watch List Rank: 46
Source of Persecution: Organised corruption/ Tribal antagonism/ Secular intolerance
Earlier in the month CSW was in Washington DC hosting representatives from faith organisations in Colombia; the Colombian Council of Evangelical Churches (CEDECOL); Justapaz, an NGO linked to the Mennonite Church; and Corsoc, a regional NGO in the north of the country linked to the Association of Evangelical Churches of the Caribbean (AIEC).
They met with US Congressional offices and the State Department to publicly support for the ongoing peace process with the FARC.
The meeting was also designed to encourage others to put pressure on the Colombian government to put in place policies to address the internal armed conflict.
It is thought that all actors in the armed conflict are responsible for major human rights violations, including the removal of religious freedom.
In Colombia hundreds of church leaders have been victim to targeted attacks over the past 16 years.
CSW and other groups hope the truth and reconciliation process that has been built into the peace agreement will clarify thousands of open murder cases and disappearances.
CSW's Chief Executive Mervyn Thomas said: "We welcome the news of a bilateral ceasefire agreement between the FARC and the government which includes a plan for the demobilisation of FARC guerrillas.
"This represents an important step forward in bringing an end to a conflict that has left millions of victims over more than half a century of conflict.
"We support the call of our partners to the Government of Colombia to also pursue effective policies to address the other actors in the conflict, including the ELN and neo-paramilitary groups, both of which are responsible for ongoing human rights violations, including violations of freedom of religion or belief."