Up to 700 guerrillas refused to join the peace process and remained armed in dozens of municipalities around the country.
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The report from Bogota stated that dissidents were to be bombed as they refused to join the landmark peace deal signed nearly a year ago.
About 7,000 guerrillas from FARC handed their weapons over to the UN following peace talks in Cuba between 2012 and 2016.
FARC leaders had already expelled the dissidents from the organisation before the peace deal was signed on Nov. 24, 2016.
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Colombia’s Defence Ministry considered the dissidents to be part of drug-trafficking networks, which was previously bombed by the national army.
Meanwhile, the army stopped bombing positions held by the National Liberation Army (ELN), a smaller guerrilla movement that agreed to a temporary ceasefire from Oct. 1 until mid-January.
The ELN admitted to breaking the ceasefire on Oct. 17 when the group killed an indigenous leader whom it accused of being a spy for the government in the western region of Choco.
The government said the violation did not affect the continuation of the ceasefire.
The peace deal with FARC and the ongoing talks with the ELN followed more than five decades of conflict in Colombia involving the two leftist rebel movements, the army and right-wing paramilitary groups.
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More than 260,000 people were killed and millions displaced in the conflict.
