By Matthew Cole and Brian Ross

CIA officials caused the deaths of an American mother and child in a tragic plane shootdown above Peru, according to a blistering new report, by operating a counter-drug program outside the rules for six years and then lying about it to their superiors.

The report also says that after Roni Bowers and her daughter Charity died, the officials tried to cover up how it happened by "repeatedly" lying to Congress. Details from the report, and footage from the 2001 shootdown, are featured in this week's edition of "Brian Ross Investigates."

The CIA inspector general's report details "an environment of negligence" in which nearly two dozen officials knowingly participated in the shootdown of the Bowers plane and 14 other aircraft over the Peruvian jungle between 1996 and 2001 without following the established rules. While the program was in operation, according to the report, the officials misled their superiors and the National Security Council about the procedures being followed, and assured them that no planes were being shot down until it was certain they were drug planes.

After the Bowers shoot down in April 2001, according to the report, the officials tried to cover up their mistakes by "misrepresent[ing] the Agency's performance [in]almost a dozen Congressional briefings and hearings." The report cites numerous violations, omissions, and falsehoods, and even suggests that the CIA's general counsel interfered with a Department of Justice investigation into the shootdown. The Department of Justice said it would prosecute the officials for lying and the deaths of Roni and Charity Bowers, according to the report, if the CIA did not work out an "administrative" plan to discipline them.

On April 20, 2001, Jim and Veronica "Roni" Bowers and their two children, six-year-old son Cory and infant daughter Charity, were returning to their home in Peru from a trip to Brazil in a small airplane piloted by Kevin Donaldson.

The Bowers' worked as Christian missionaries along a stretch of the Amazon River near Iquitos, Peru, a remote jungle region near the Brazilian and Colombian borders heavily traveled by drug traffickers.

The CIA and the Peruvian Air Force were working in the same area, trying to interdict drug smugglers. Starting in 1995, they'd operated a joint program to intercept civilian aircraft suspected of smuggling drugs from South America to the U.S., shooting them down if necessary.

A CIA spotter plane saw the Cessna in which the Bowers family was flying and alerted the Peruvian Air Force, which shot them down, killing Roni and Charity. Jim Bowers, Cory and pilot Kevin Donaldson survived after their plane crash-landed .

The so-called Airbridge Denial Program (ABDP) shot down a total of 15 aircraft between 1995 and 2001, all of them except the Bowers' reportedly piloted by drug smugglers. The program had to be authorized by an executive order from President Bill Clinton in 1994 because of international laws prohibiting firing on civilian planes. Offiicials were supposed to follow a series of steps to differentiate between an innocent passenger plane and a drug plane before shooting any aircraft down, but did not follow those steps on April 20, 2001 or in 13 of the other 14 cases, according to the report.

The IG report blames the Peruvian Air Force for the misidentification of the Bowers' plane, but says the CIA should have been able to call off the shootdown if it had followed the program's official guidelines. Investigators also found evidence that CIA officials running the program ordered a Peruvian Air Force jet to strafe suspected drug smugglers who fled their aircraft after it had been shot down, which was both contrary to guidelines.

CIA Tape of Plane Shootdown

The nearly two-hour long encounter between the Bowers family and the CIA and the Peruvian Air Force on April 20, 2001 was captured in a CIA videotape.

The CIA spotter plane, with two operative aboard, sneaked up behind the Cessna as it flew over the Amazon.

"We are trying to remain covert at this point," one of the CIA pilots on the plane can be heard to say on the tape.

The CIA pilot describes the aircraft as a high-wing, single-engine float plane, which is accurate, that it has picked up on the border between Peru and Brazil.

But the CIA personnel misidentified the craft as a drug plane. The CIA alerted the Peruvian Air Force, which scrambled an interceptor. Over the next two hours, the CIA personnel would express doubts, but would not correct their error, and would repeatedly violate what the White House believed to be strict rules of engagement.

Said former counterterrorism czar Richard Clarke, who served in the White House at the time on the National Security Council, which created the anti-drug program, "Either the CIA spotter aircraft or the interceptor is supposed to get up close, identify the plane from the tail number, try to indicate to the plane that it should follow them to the ground."

That did not happen. Instead, the decision was made not to try to identify the tail number, because it might allow the plane to escape.

"You know, we can go up attempt the tail number," says a CIA operative on the tape. "The problem with that is that if he is dirty and he detects us, he makes a right turn immediately and we can't chase him."

When the Peruvian Air Force jet arrived it issued a warning to the target plane, saying, 'We will shoot you down." The warning was in Spanish, which the Bowers and their pilot could understand, but it was on the wrong frequency.

'They're Killing Us'

The CIA pilots begin to have doubts. "This guy doesn't, doesn't fit the profile," says one. But nothing was done to pull the plane back.

The CIA then asks a Peruvian Air Force liaison, "Are you sure is bandito? Are you sure?" "Yes, okay," says the Peruvian. "If you're sure," responds the CIA operative. Then more serious doubts were quietly whispered.

"That is bullshit," says one CIA operative. "I think we're making a mistake." "I agree with you," says the other operative.

A minute and a half later the gunships opened fire and the Bowers' pilot, Donaldson, screamed in Spanish for the jet to stop.

"They're killing me. They're killing us," yells Donaldson on the tape.

"Tell him to terminate," says one of the CIA operative to the Peruvian liaison. " No. Don't Shoot. No more, no mas."

The Peruvian liaison starts yelling at the pilot, "Stop! No mas, no mas, Tucan no more."

"God," says one of the CIA pilots.

By then the damage was done. Trailing black smoke, it headed for a river to land, with Roni and Charity already dead from bullet wounds and the pilot wounded in both legs.

CIA Misled Congress

Jim Bowers, his son Cory and Kevin Donaldson survived. But for almost nine years, the CIA misled Congress, the White House and the dead woman's parents about how and why the agency defied the rules established to make sure innocent people were not killed.

The CIA's internal report was completed in August 2008, seven years after the deadly incident but withheld from public disclosure. Retiring Congressman Pete Hoekstra, R.-Mich., who was ranking minority member of the House Intelligence Committee, fought for years with CIA over what he suspected was an agency cover-up.

In February, ABC News first reported that roughly 16 CIA officials were subjected to an accountability panel, which led to no dismissals or demotions.

"If there's ever an example of justice delayed, justice denied, this is it," said Rep Hoekstra, "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."

A CIA spokesperson issued a statement to ABC News in February that placed the blame for the shootdown on the Peruvian Air Force, and said its own internal review had shown no evidence of a cover-up.

"The program to deny drug traffickers an "air bridge" ended in 2001 and was run by a foreign government," said the spokesperson. "CIA personnel had no authority either to direct or prohibit actions by that government. CIA officers did not shoot down any airplane. In the case of the tragic downing of [April 20th] 2001, CIA personnel protested the identification of the missionary plane as a suspect drug trafficker."

"This was a tragic episode that the Agency has dealt with in a professional and thorough manner," continued the statement. "Unfortunately, some have been willing to twist facts to imply otherwise. In so doing, they do a tremendous disservice to CIA officers, serving and retired, who have risked their lives for America's national security."