US agency denied covering up botched anti-drug operation that led to death of American woman and baby in 2001

Harrowing CIA footage has been broadcast of the shooting down of a light aircraft carrying American missionaries in an incident the agency has been accused of covering up for nine years.

Veronica Bowers and her adopted baby, Charity, were killed by a jet's bullets in 2001 after the CIA and a Peruvian fighter mistook the aircraft in which they were travelling for a drug plane. As the Guardian reported at the time, the incident was initially blamed on trigger-happy Peruvian authorities but an inquiry was launched in the US after it emerged that a US surveillance team had wrongly identified the missionaries' plane.

The awful truth of what occurred is played out in a CIA video of the incident filmed from surveillance plane involved.

"I think we're making a mistake," one CIA operative is heard to say in the film after alerting the Peruvian airforce to the plane. "I agree with you," another says.

They express their doubts to the pilot of Peruvian fighter jets, but they appear to fail to understand them.

CIA officers are heard trying in vain to communicate their doubts in broken Spanish. "I don't know if this is bandito or amigo," an officer is heard to say. He urges a Peruvian official to get the plane to land before opening fire – which he communicates by make the sound of a machine gun firing.

Later in the film, obtained by the US broadcaster ABC, the pilot of the missionary's plane, Kevin Donaldson, is heard communicating in Spanish with a control tower in the area. He apparently did not hear a warning from Peruvian airforce because he was using a difference frequency.

"I'm at 4,000 feet. The military is here. I don't know what they want," Donaldson says.

Moments later the jets open fire and Donaldson is heard screaming: "They're killing me! They're killing me!"

The CIA operatives are then heard to say "tell them to terminate, don't shoot". But by then it was too late. Bowers and her daughter were killed by a bullet from the jet's guns.

The plane then crash landed. Donaldson, Bowers's husband, Jim, and the couple's son survived.

The CIA denied it had covered up what took place. "This was a tragic episode that the agency has dealt with in a professional and thorough manner," it said in a statement.

But a Republican congressman, Pete Hoekstra, who has campaigned on the issue, insisted the CIA still had questions to answer. "The [intelligence] community's performance in terms of accountability has been unacceptable. These were Americans that were killed with the help of their government, the community covered it up, they delayed investigating."