President Ivan Duque said the helicopter he was flying in Friday near the border with Venezuela was hit by gunfire in the first attack against a Colombian head of state in nearly 20 years.
No one was injured, and authorities did not say which side of the border the shots came from. Colombia regularly accuses Venezuela of harboring Colombian rebels on its territory.
"It is a cowardly attack, where you can see bullet holes in the presidential aircraft," Duque said in a statement.
Duque said he was flying with the defense and interior ministers and the governor of Norte de Santander province, which borders Venezuela, when the helicopter was attacked.
Photos released by the president's office showed the tail and main blade had been hit.
Duque said the aircraft's "safety features" prevented a "lethal" attack.
"I have given very clear instructions to the entire security team to go after those who shot at the aircraft," he said.
The US, European Union and UN mission in Colombia all condemned the attack.
The presidential delegation had left the town of Sardinata and was headed to the border city of Cucuta when they came under fire.
Duque had attended an event in the Catatumbo region, one of the main coca-growing areas of the country. Colombia is the world's largest cocaine producer.
Holdouts from the disbanded FARC rebel group, an active guerrilla group called the National Liberation Army (ELN), and other armed bands fight drug trafficking turf wars along the long and porous border with Venezuela.
The two countries broke off relations after Duque, a conservative, came to power in 2018. Venezuela is governed by socialist President Nicolas Maduro.
The Duque government has repeatedly accused Venezuela of giving refuge to ELN fighters.
"We are not frightened by violence or acts of terrorism. Our state is strong and Colombia is strong to confront this kind of threat," Duque said after the attack on his chopper.
The border area has been violent of late.
- Anger in the streets -
On June 16, a car bomb exploded on a military base in Cucuta, wounding 36 people.
The government blamed the ELN, with which it ended peace negotiations in 2019.
Those talks started after the government concluded a historic peace accord in 2016 with the much bigger FARC that ended decades of civil war.
The last attack against a president in Colombia was a bombing that targeted then leader Alvaro Uribe in 2003.
A 20-kilogram (44-pound) bomb hidden in a building near the airport in the southwest city of Neiva exploded prior to the landing of a plane carrying Uribe, who is Duque's political mentor.
The blast killed 15 people and wounded 66. The government blamed the FARC for that attack.
Since Duque came to power the country has been enduring its worst outbreak of violence since the peace accord with the FARC.
The government accuses armed groups financed with drug money of carrying out massacres in isolated coca- producing regions.
With his approval record at rock bottom, Duque is also facing anger in the streets.
Tens of thousands of people voiced their discontent on April 28 against a proposed tax hike that they said would hurt the middle class, already suffering economically from the pandemic.
The government withdrew the proposal, but the protests morphed into a broader grassroots movement to air gripes about inequality, education and other woes, amid complaints of heavy handed police action to put down the marches. More than 60 people have died in the unrest.