WASHINGTON — The U.S. military says it flew thousands of spy flights over Colombian jungles trying to find and free three Pentagon contractors since their kidnapping in 2003.

In the end, it was a daring operation by Colombian military intelligence agents that finally rescued the American trio from leftist rebels.

Until this week’s rescue, some U.S. government officials despaired that Tom Howes, Marc Gonsalves and Keith Stansell might ever be freed. Some counterterror, military and diplomatic officials familiar with Bush administration efforts to secure their release questioned whether enough was being done.

The American connection

On Thursday, Col. William Costello, spokesman for the U.S. Southern Command, said the command made 3,600 intelligence, surveillance and reconnaissance flights, followed up on 175 intelligence leads and spent $250 million trying.

“We’ve been actively searching for these guys every day for the past five and a half years,” Costello said.

FBI spokesman Richard Kolko said the agency sent crisis negotiators and investigators on “countless trips to Bogota” since the kidnapping.

One official said a Defense Intelligence Agency cell that primarily works to track captured or missing U.S. troops has been working on the case of the civilian contractors, who had been held by the FARC, since their drug-surveillance plane went down in the jungle in February 2003.

Another said it was U.S. intelligence that located the hostages.

A third said the U.S. Special Operations Command helped with surveillance that positively located the hostages within the past year using satellites, aircraft and ground reconnaissance — and had tracked them since then.

All three spoke on condition of anonymity because they were not authorized to speak on the record and the Bush administration was adamant about giving the Colombians the credit.

“This was a Colombian-planned and Colombian-executed operation,” State Department spokesman Sean McCormack told reporters. “We were in a supporting role.”

Officials have said the U.S. and Colombian governments have known the location of the hostages a number of times over the years — and planned rescue missions several times. But they didn’t attempt them because of the difficulty of the jungle terrain and the risk that the hostages could be killed.

Finally, it was a trick by Colombian spies that persuaded the rebels to hand over the men, along with kidnapped presidential candidate Ingrid Betancourt and 11 others on Wednesday.

Colombian Defense Minister Juan Manuel Santos said military intelligence agents infiltrated the guerrilla ranks and led the local commander in charge of the hostages to believe they were being taken to the guerrillas’ supreme leader.

The reluctance of U.S. officials to highlight the U.S. role may be a reflection of American politics.

Congressional support for Plan Colombia — the multibillion-dollar U.S. aid package to Colombia to help it fight its war on drugs and the insurgency — has rested heavily on promises that no U.S. troops would be put at risk and drawn into a jungle war with rebels, said George Withers, senior fellow with the Washington Office on Latin America, a human rights advocacy organization.

Two keys to the mission

The mission’s success hinged entirely, its Colombian planners said Thursday, on a near-total breakdown in communications between the isolated guerrilla jailers and their commanders — the net result of years of intense U.S.-Colombian military cooperation that has seriously weakened Latin America’s last major rebel army.

This breakdown in the chain of command has made it easier to flip disillusioned rebels to the government’s side, and indeed, Padilla said more than one double agent was involved in this mission.

A Colombian army general, speaking on condition of anonymity, said a disgruntled member of FARC had agreed to spearhead the operation. This turncoat, he said, was trusted by both the rebels’ high command and by the leader of the 1st Front, which was holding the hostages.

The turncoat was upset with the FARC because his own commander had taken a house and farm away from him, the general said. This was payback.

He convinced Gerardo Aguilar Ramirez, alias Cesar, the commander of the 1st Front, that top commanders wanted the 15 hostages moved to a rallying point, the general said.

U.S. spy satellites helped track the hostages on a monthlong journey that began May 31 and ended with Wednesday’s rescue.

How the raid was carried out

On Tuesday, the two Russian-made Mi-17 helicopters left a military base in an Andean mountain valley, settling down for a nervous night in a wilderness clearing.

Aboard were four air force crewmen in civilian disguise, seven military intelligence agents and the guerrilla turncoat, military officials said. Two of the agents were dressed as rebels, and the rest wore white, as if representing some sort of humanitarian mission.

All had taken a week and a half of acting lessons, said Gen. Freddy Padilla, Colombia’s armed forces chief.

Shortly after midday Wednesday, the helicopter touched down at the rendezvous point.

One of the agents, posing as a cameraman, recorded video as the guerrillas on the ground bound the hostages’ hands on the crew’s instructions, Padilla said. Tying up the hostages was part of the plan.

“These are 14 trained soldiers we’re dealing with,” Padilla said, referring to the captive Americans and 11 Colombian soldiers or police. “Nobody wanted to risk them trying to overpower the crew.”

Once aloft, it was Cesar and his aide who were overpowered instead.