Iván Duque Márquez and others were flying through Colombia's Catatumbo region toward the city of Cucuta, Norte de Santander province capital, when gunfire opened on the helicopter. Mr Duque called the attack “cowardly”, and a spokesman for the presidency reported no one was injured.
The President announced security personnel have been given clear instructions to find those behind the attack on the helicopter.
Speaking after the shooting, the President added: “I want to inform the country that after fulfilling a commitment in Sardinata, in Catatumbo and approaching to land in the city of Cúcuta, the presidential helicopter was the victim of a attempt.
“Both the aerial device and the aircraft’s capacity prevented something lethal from happening. It’s a cowardly attack.
“Once again, we reiterate that as a Government we will not faint a single minute, a single day, in the fight against drug trafficking, the terrorism and organised crime organisations that operate in the country.”
Mr Duque also insisted “Colombia is strong to face these threats” of violence.
The helicopter was also carrying Defence Minister Diego Molano, Interior Minister Daniel Palacios, and governor of Norte de Santander Silvano Serrano.
According to local media, there is currently a “Padlock operative” in the Camilo Daza neighborhood, from where the presidential helicopter was shot.
It is unknown who carried out the attack.
Mr Duque is Colombia’s most unpopular president ever, according to a Invamer poll.
A telephone survey of 1,200 people found 76 percent of respondents disapproved of his performance as President.
It beat the previous record of 74 percent disapproval set by conservative Andres Pastrana, who was president from 1998 to 2002 and led failed peace negotiations with leftist fighters.
Mr Duque’s popularity plummeted since social unrest broke out at the end of April, initially over a now-abandoned tax reform plan.
Earlier in June, a car bomb was detonated at a military base used by the 30th Army Brigade in Cucuta.