The U.S. military has been forced to relocate a large fleet of drones from a key counterterrorism base on the Horn of Africa after a string of crashes fanned local fears that the unmanned aircraft were at risk of colliding with passenger planes, according to documents and interviews.

Air Force drones ceased flying this month from Camp Lemonnier, a U.S. installation in Djibouti, after local officials expressed alarm about several drone accidents and mishaps in recent years. The base serves as the combat hub for counterterrorism operations in Yemen and Somalia, playing a critical role in U.S. operations against al-Shabab, the Somali Islamist militia that has asserted responsibility for the Nairobi shopping mall attack, which killed more than 60 people.

The Pentagon has temporarily moved the unmanned aircraft from the U.S. base in Djibouti’s capital to a makeshift airstrip in a more remote part of the country. U.S. military officials said the disruption has not affected their overall ability to launch drone strikes in the region, but they declined to say whether it has forced them to curtail the frequency of drone missions or hindered their surveillance of al-Shabab camps and fighters.

The Djiboutian government’s growing unease over drone flights casts doubt on its commitment to host the aircraft over the long term. It is unclear whether the temporary drone base can be transformed into a permanent home or whether the U.S. military will have to hunt for another site in the region, according to previously undisclosed correspondence between the Defense Department and Congress.

That uncertainty raises fresh questions about the Pentagon’s plan to invest more than $1 billion to upgrade Camp Lemonnier into a major regional base, supporting operations throughout Africa, as well as in parts of the Arabian Peninsula and Indian Ocean. Those plans include a $228 million compound to house up to 700 personnel from the highly secretive Joint Special Operations Command.

An end to drone flights from Camp Lemonnier, Djibouti

More broadly, however, the concerns about drone safety present a strategic challenge for the Pentagon as it begins to shift more of the robot planes to new frontiers, where they must share congested airspace with commercial aircraft.

A rash of accidents

Unlike in the war zones in Afghanistan and Iraq, where the U.S. military essentially has ruled the skies, the drones in Djibouti and other foreign locations have flown from the same runways and relied on the same air traffic controllers as civilian pilots.

At least five drones based at Camp Lemonnier have crashed since January 2011, Air Force records show, including one that plowed into the ground next to a neighborhood in Djibouti’s capital, which goes by the same name as the country.

Last year, the Pentagon was forced to suspend drone operations in Seychelles, an island nation in the Indian Ocean, after two Reaper drones crashed on the runway at the main international airport, which serves half a million passengers a year.

The overseas accidents could have repercussions in the United States, where the military and the drone industry are pressing the federal government to open up the skies to remote-controlled aircraft.

Under a law passed by Congress last year, the Federal Aviation Administration is preparing rules that would integrate drones into U.S. airspace by the end of 2015. Until then, the Defense Department can fly drones at home only in restricted military airspace or with special permits.

In Djibouti, a tiny and parched African country that borders the Red Sea and the Gulf of Aden, the government notified the Obama administration early this year that it was concerned about a series of drone accidents and near-misses. It was time, Djiboutian officials said, to find another home for the aircraft.

Short-term fix

The U.S. military intensified its drone operations at Camp Lemonnier in 2011 as part of a crackdown against al-Qaeda targets in nearby Yemen and Somalia, with up to 16 takeoffs and landings each day.

But elbowroom was at a premium. The base was already crammed with military fighter jets, cargo planes and other manned aircraft. Lemonnier is shoehorned onto a stretch of shore front and shares a single runway with Djibouti’s only international airport for commercial flights. French and Japanese troops also have small bases next to the airport, alongside the Djiboutian military.

Rattled by the rash of drone crashes, the Djiboutian government asked the Pentagon to move its unmanned aircraft away from the city to a rarely used airstrip in the desert, Chabelley Airfield, according to the unclassified documents, which were obtained by The Washington Post as part of a public records request.

In a letter to Congress in February, the Pentagon asked for urgent authorization of $13 million in funds and equipment to build “minimal facilities necessary to enable temporary operations” at Chabelley. To save time on construction, the military used troop labor instead of private contractors.

“The construction is not being carried out at a military installation where the United States is reasonably expected to have a long-term presence,” the documents stated. “No decisions have been made about long-term [drone] operations in the region.”

The military gradually transferred the drone operations to Chabelley and flew the last drone flight from Lemonnier this month, U.S. defense officials said.

Air Force Maj. Matt Hasson, a spokesman for a U.S. counterterrorism task force that oversees most military operations at Camp Lemonnier, declined to comment when asked whether the move had hindered drone operations in Yemen or Somalia. But he said that basing the drones at Chabelley “enables us to continue to fully support our partners to secure their borders against illegal activities.”

Airport safety ‘paramount’

The U.S. government has a fixed, long-term lease for Camp Lemonnier and pays Djibouti $38 million a year in rent. Djiboutian officials said that they were happy with their military partnership with Washington but that the armed Predator and Reaper drones were flying — and crashing — too close to their capital for comfort.

“The safety of the airport is paramount,” said Roble Olhaye, Djibouti’s ambassador to the United States. “The airport seems to be congested. There are so many military aircraft based at the airport and around the airport — French aircraft, American aircraft, Japanese aircraft.”

He said that U.S. and Djiboutian officials were still discussing possible long-term solutions but that Chabelley was “the best option available at the moment, for them, for us.”

“It gives them the necessary leeway, the necessary space,” Olhaye said. “I think it’s in the best interest for all.”

The presence of the unmanned aircraft remains a sensitive subject in Djibouti. During a telephone interview, Olhaye shied away from using the term “drone,” chuckling whenever a reporter mentioned it.

In a separate interview, a diplomat from a Middle Eastern country cited rising concern that the civilian side of the Djibouti airport might be targeted by militants looking to retaliate against U.S. drone operations. Regional tensions have risen as the U.S. military’s Joint Special Operations Command has carried out dozens of strikes against al-Qaeda-affiliated groups in Yemen.

“Once you have military installations in civilian facilities, that civilian facility and the public become endangered,” the diplomat said, speaking on the condition of anonymity to discuss U.S. drone strategy in the region.

The same potential problem exists elsewhere.

In Ethi­o­pia, for example, the Air Force flies Reaper drones from a civilian airport in the town of Arba Minch. In West Africa, the Air Force began flying Predator drones in February from a small military base in Niger that abuts the capital’s international airport.

Within two months, one of them had crashed while on a surveillance mission in neighboring Mali, according to Air Force records.