Pastor Plinio Rafael Salcedo, who was a church leader within the Movimiento Misionero Mundial group of churches, was found dead at his home in the village of La Caucana on Saturday, according to religious freedom charity Christian Solidarity Worldwide (CSW).
Currently, the motive for the attack is unclear but some suspect it may be linked to peace protests that took place two days prior to the incident.
1000 people from local Protestant and Catholic churches gathered last week, to call for the restoration of peace in the region.
The country has been in conflict for over 50 years as guerrillas, government and paramilitary forces have fought for power in the region.
Throughout this time hundreds of church leaders have been targeted for assassination by all sides.
Illegal armed groups often attempt to force the cooperation of church leaders in an effort to bring the entire community under their authority.
CSW's Chief Executive Mervyn Thomas said: "We extend our heartfelt condolences to the family of Pastor Plinio Rafael Salcedo.
"Whilst we welcome the Colombian government's efforts regarding the peace agreement so far, little has changed for many communities in regions where illegal armed groups continue to operate with impunity.
"We call on the Colombian government to conduct a full investigation into the murder of the pastor and to bring those responsible to justice. We also urge the government to work with civil society organisations and churches to ensure lasting peace to Colombia."
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.