U.S. surveillance operations in Africa are dependent on permission from countries willing to host bases for the spy planes. In exchange, those countries usually insist that the Americans share intelligence gleaned from the skies.

Such arrangements have the potential to go awry, especially in Africa, where many countries have poor human rights records. U.S. officials said they take care to withhold intelligence that could enable their African partners to target political opponents instead of terrorist groups, but they acknowledged that it can be difficult to know the difference.

“The challenge always is, what’s the sharing relationship with the nation where these assets are based?” said a senior U.S. military official familiar with the operations. “If I gave you information that I could reasonably expect you to act upon, then I bear some responsibility for the consequences.”

In general, the U.S. military is prohibited from disclosing information about a surveillance target to an African country unless the Americans would be permitted under their own laws to take action, said the senior military official, speaking on the condition of anonymity to discuss intelligence matters.

In a written reply to questions from The Washington Post, U.S. Africa Command said it obtains permission for surveillance flights from national governments in a process coordinated by the State Department. If an African country were hostile or unwilling, spy flights could still occur but would need to be approved at the highest levels — either by the U.S. president or the defense secretary.

The U.S. military’s biggest partner in the regional hunt for Joseph Kony, the leader of the guerrilla group known as the Lord’s Resistance Army, is the Ugandan People’s Defense Force. The force has deployed thousands of soldiers to South Sudan and the Central African Republic to look for him and his followers. Ugandan military officials said their operations were guided by intelligence received from the United States and other countries, but they declined to say how that intelligence was gathered.

“It is not for media consumption,” said Col. Joseph Balikuddembe, commander of the Ugandan forces looking for Kony.

According to a U.S. diplomatic cable written shortly after American contractors began searching for Kony, the Ugandan government reached an oral agreement with U.S. officials, pledging to observe “the principles of proportionality, distinction and humane treatment of captured combatants” when using American intelligence to pursue the Lord’s Resistance Army.

“Uganda understands and acknowledges that misuse of this intelligence could cause the U.S. to end this intelligence-sharing relationship,” read the Dec. 16, 2009, cable, which was signed by Jerry P. Lanier, the American ambassador to Uganda.

The cable stated that U.S. intelligence reports about the Lord’s Resistance Army would be filtered and reviewed by an American military officer at a “Combined Intelligence Fusion Center” in Kampala, the capital, before passing them to the Ugandan military.

Human rights groups have accused Ugandan President Yoweri Museveni of tolerating extrajudicial killings of political opponents and other human rights violations.

But Lanier wrote in his 2009 cable that he had received a promise from Crispus Kivonga, the Ugandan defense minister, that his country would not abuse U.S. intelligence. The ambassador said he found the reassurance “both reliable and credible.”

The U.S. military acknowledged that it is receiving help from contractors in the hunt for Kony but has declined to identify the firms or describe their duties as part of the mission, code-named Tusker Sand.

“We have U.S. contractors in support of our operations but not directly supporting the operations of our partner nations,” said Capt. Kenneth S. Wright, a Navy SEAL who commands about 100 elite U.S. troops who have been deployed to central Africa.

A contractor who formerly worked on Tusker Sand, however, said Ugandan and Congolese military officers — but no U.S. military personnel — rode along on all surveillance flights. Most of the flights originated from the Entebbe airport for missions over Congo, the Central African Republic and South Sudan.

The African officers would communicate by radio with their respective forces on the ground as the Pilatus PC-12 spy plane hovered above.

Surveillance targets were chosen by U.S. military units based at Africa Command headquarters in Stuttgart, Germany, and at RAF Molesworth, a key U.S. intelligence hub in Britain. African and American military officers frequently argued over the targets, however, with the Africans complaining that U.S. intelligence on rebel movements was outdated, according to the former contractor, who spoke on the condition of anonymity to discuss sensitive operations.

In its written response to The Post, Africa Command acknowledged that “we have the authority for host nation personnel to ride along” on the surveillance flights but declined to give details.

Although the U.S. military can field highly advanced surveillance technology, African security forces are often surprised to learn that there are limits to what the Americans can see.

“They really do believe that we know a lot more than we really do,” said the senior U.S. military official. “There is this sense that we’re Oz, we know everything all the time.”