The fatal episode occurred in April 2001 over the remote Amazon forest of Peru. The C.I.A. had been operating in the region as part of a joint counternarcotics mission with the Peruvian Air Force, which had the authority to intercept or shoot down planes that did not comply with orders to land. Government reports after the shooting attributed the accident in part to language barriers that prevented the pilot from understanding the orders.

The plane was carrying two missionaries, Veronica Bowers and her husband, James Bowers, their two children, and a pilot. Ms. Bowers’ husband and the couple’s son survived the crash, along with the pilot. Any decision to re-examine the matter could be an early test for the Justice Department under an Obama administration. If the Justice Department determines there was wrongdoing, it may have no choice about whether to pursue a prosecution. At the same time, a lengthy investigation into C.I.A. wrongdoing could immediately chill the relationship between the White House and the spy agency at a time when the C.I.A. is central to the American campaign against terrorism.

According to Mr. Helgerson’s report, C.I.A. officials “within hours” of the downing explained the accident as a one-time mistake in an otherwise sound counternarcotics program.

“In fact, this was not the case,” the report said. It said that the C.I.A. repeatedly misled the White House and Congress between 1995 and 2001 about the Peru operation.

The inspector general’s report said that after the downing of the missionaries’ plane, the C.I.A. had conducted internal reviews “that documented sustained and significant violations of required intercept procedures.” But it said that the agency had denied Congress, the Department of Justice and the National Security Council access to these findings.

Mr. Hoekstra said Thursday that the inspector general’s investigation specifically named C.I.A. officials responsible for the alleged cover-up, but he declined to name those officers. The Justice Department and the C.I.A. inspector general had been investigating the roles played in the incident by the agency’s field officers in Latin America as well as senior officials at the agency’s headquarters in Virginia.

It is also possible that C.I.A. lawyers could face scrutiny if the Justice Department decides to reopen the Peru investigation. The report by Mr. Helgerson says that C.I.A. lawyers from the office of the general counsel “advised agency managers to avoid written products lest they be subject to legal scrutiny” in connection with the downing of the plane.