Five former Blackwater guards have been indicted in federal court on charges related to the 2007 episode.

A spokeswoman for Xe did not respond to a request for comment.

For its intelligence work, the company’s sprawling headquarters in North Carolina has a special division, known as Blackwater Select. The company’s first major arrangement with the C.I.A. was signed in 2002, with a contract to provide security for the agency’s new station in Kabul, Afghanistan. Blackwater employees assigned to the Predator bases receive training at Nellis Air Force Base in Nevada to learn how to load Hellfire missiles and laser-guided smart bombs on the drones, according to current and former employees, who asked not to be identified for fear of upsetting the company.

The C.I.A. has for several years operated Predator drones out of a remote base in Shamsi, Pakistan, but has secretly added a second site at an air base in Jalalabad, Afghanistan, several current and former government and company officials said. The existence of the Predator base in Jalalabad has not previously been reported.

Officials said the C.I.A. now conducted most of its Predator missile and bomb strikes on targets in the Afghanistan-Pakistan border region from the Jalalabad base, with drones landing or taking off almost hourly. The base in Pakistan is still in use. But officials said that the United States decided to open the Afghanistan operation in part because of the possibility that the Pakistani government, facing growing anti-American sentiment at home, might force the C.I.A. to close the one in Pakistan.

Blackwater is not involved in selecting targets or actual strikes. The targets are selected by the C.I.A., and employees at the agency’s headquarters in Langley, Va., pull the trigger remotely. Only a handful of the agency’s employees actually work at the Predator bases in Afghanistan and Pakistan, the current and former employees said.

They said that Blackwater’s direct role in these operations had sometimes led to disputes with the C.I.A. Sometimes when a Predator misses a target, agency employees accuse Blackwater of poor bomb assembly, they said. In one instance last year recounted by the employees, a 500-pound bomb dropped off a Predator before it hit the target, leading to a frantic search for the unexploded bomb in the remote Afghan-Pakistani border region. It was eventually found about 100 yards from the original target.

The role of contractors in intelligence work expanded after the Sept. 11 attacks, as spy agencies were forced to fill gaps created when their work forces were reduced during the 1990s, after the end of the cold war.