Petro's new left-wing government has focused on changing the tactics used by the military, demanding that they show more respect for human rights and act in defense of peace.
Petro has reopened dialogue with the National Liberation Army (ELN), which is widely recognized as the last organized guerrilla group operating in the South American country.
His predecessor, the conservative Ivan Duque, had broken off peace talks following a 2019 car bomb attack on a police academy in Bogota that left 22 people dead.
Petro has also proposed a "multilateral" ceasefire with dissidents from the Revolutionary Armed Forces of Colombia (FARC) that laid down arms and signed a peace deal in 2016.
The president has sought a "total peace" policy in a bid to end the conflict.
And he has also proposed the "peaceful dismantling" of other organizations such as the Clan del Golfo, the country's largest drug cartel, which has announced its willingness to coordinate a ceasefire to negotiate its disarmament.
"These actions demonstrate a clear sabotage of the total peace," said Petro of the attack on Friday.
The UN special representative in Colombia, Carlos Ruiz, also condemned the attack and called to "continue insisting on the efforts around peace".
Defense minister Ivan Velasquez called on the armed forces to "respond forcefully to this attack on peace."