This is the first time in 20 years that a Colombian leader has come under attack in a country that's struggling to contain rebel groups.
Columbia's President Ivan Duque said the helicopter he was flying was hit by gunfire near the border with Venezuela in the first attack against a Colombian head of state in nearly 20 years.
No one was injured in the incident on Friday, and authorities did not say which side of the border the shots came from. Colombia regularly accuses Venezuela of harbouring 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.
The last attack against a president in Colombia was a bombing that targeted then leader Alvaro Uribe in 2003.
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.
#Colombia 🎥 Así quedó el helicóptero de la Fuerza Aérea colombiana tras el atentado al Presidente @IvanDuque y dos de sus ministros.— Cima360 (@cimanewsdigital) June 26, 2021
La aeronave recibió 6 disparos que dañaron el armazón sin lograr perforarlo.
✍🏻 @CarolaBriceno pic.twitter.com/E2f7tyIfPp
"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.