A joint program, part of a U.S. covert operation, reflects the enduring alliance between Saudi Arabia and the U.S. even as their relationship and the kingdom’s place in the region are in flux.

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WASHINGTON — When President Obama secretly authorized the CIA to begin arming Syria’s embattled rebels in 2013, the spy agency knew it would have a willing partner to help pay for the covert operation. It was the same partner the CIA has relied on for decades for money and discretion in far-off conflicts: the Kingdom of Saudi Arabia.

Since then, the CIA and its Saudi counterpart have maintained an unusual arrangement for the rebel-training mission, which the Americans have code-named Timber Sycamore. Under the deal, current and former administration officials said, the Saudis contribute weapons and large sums of money, and the CIA takes the lead in training the rebels on AK-47 assault rifles and tank-destroying missiles.

The support for the Syrian rebels is only the latest chapter in the decades-long relationship between the spy services of Saudi Arabia and the United States, an alliance that has endured through the Iran-contra scandal, support for the mujahedeen against the Soviets in Afghanistan and proxy fights in Africa. Sometimes, as in Syria, the two countries have worked in concert. In others, Saudi Arabia has simply written checks underwriting U.S. covert activities.

The joint arming and training program, which other Middle East nations contribute money to, continues as U.S. relations with Saudi Arabia — and the kingdom’s place in the region — are in flux. The old ties of cheap oil and geopolitics that have long bound the countries together have loosened as America’s dependence on foreign oil declines and the Obama administration tiptoes toward a diplomatic rapprochement with Iran.

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And yet the alliance persists, kept afloat on a sea of Saudi money and a recognition of mutual self-interest. In addition to Saudi Arabia’s vast oil reserves and role as the spiritual anchor of the Sunni Muslim world, the long intelligence relationship helps explain why the United States has been reluctant to openly criticize Saudi Arabia for its human-rights abuses, its treatment of women and its support for the extreme strain of Sunni Islam, Wahhabism, that has inspired many of the terrorist groups the United States is fighting.

The Obama administration did not publicly condemn Saudi Arabia’s public beheading this month of a dissident Shiite cleric, Sheikh Nimr al-Nimr, who had challenged the royal family.

Saudi financing

Although the Saudis have been public about their help arming rebel groups in Syria, the extent of their partnership with the CIA’s covert action campaign and their direct financial support had not been disclosed. Details were pieced together in interviews with a half-dozen current and former U.S. officials and sources from several Persian Gulf countries. Most spoke on the condition of anonymity.

From the moment the CIA operation was started, Saudi money supported it.

“They understand that they have to have us, and we understand that we have to have them,” said Mike Rogers, the former Republican congressman from Michigan who was chairman of the House Intelligence Committee when the CIA operation began. Rogers declined to discuss details of the classified program.

U.S. officials have not disclosed the amount of the Saudi contribution, which is by far the largest from another nation to the program to arm the rebels against President Bashar Assad’s military. But estimates have put the total cost of the arming and training effort at several billion dollars.

The Obama administration has embraced the covert financing from Saudi Arabia — and from Qatar, Jordan and Turkey — at a time Obama has pushed Gulf nations to take a greater security role in the region.

Spokesmen for the CIA and the Saudi Embassy in Washington, D.C., declined to comment.

When Obama signed off on arming the rebels in spring 2013, it was partly to try to gain control of the apparent free-for-all in the region. The Qataris and the Saudis had been funneling weapons into Syria for more than a year. The Qataris had even smuggled in shipments of Chinese-made FN-6 shoulder-fired missiles over the border from Turkey.

The Saudi efforts were led by Prince Bandar Bin Sultan, at the time the intelligence chief, who directed Saudi spies to buy thousands of AK-47s and millions of rounds of ammunition in Eastern Europe for the Syrian rebels. The CIA helped arrange some of the arms purchases for the Saudis, including a large deal in Croatia in 2012.

By summer 2012, a freewheeling feel had taken hold along Turkey’s border with Syria as the Gulf nations funneled cash and weapons to rebel groups, even some that U.S. officials were concerned had ties to radical groups such as al-Qaida.

The CIA was mostly on the sidelines during this period, authorized by the administration under the Timber Sycamore training program to deliver nonlethal aid to the rebels but not weapons. In late 2012, according to two former senior U.S. officials, David Petraeus, then the CIA director, delivered a stern lecture to intelligence officials of several Gulf nations at a meeting in Jordan. He chastised them for sending arms into Syria without coordinating with one another or with CIA officers in Jordan and Turkey.

Months later, Obama gave his approval for the CIA to begin directly arming and training the rebels from a base in Jordan, amending the Timber Sycamore program to allow lethal assistance. Under the new arrangement, the CIA took the lead in training, while Saudi Arabia’s intelligence agency, the General Intelligence Directorate, provided money and weapons, including TOW anti-tank missiles.

The Qataris have also helped finance the training and allowed a Qatari base to be used as an additional training location. But U.S. officials said Saudi Arabia was by far the largest contributor to the operation.

Certain expectations

While the Saudis have financed previous CIA missions with no strings attached, the money for Syria comes with expectations, current and former officials said. “They want a seat at the table, and a say in what the agenda of the table is going to be,” said Bruce Riedel, a former CIA analyst and now a senior fellow at the Brookings Institution.

The CIA training program is separate from another program to arm Syrian rebels, one the Pentagon ran that has since ended. That program was designed to train rebels to combat Islamic State group fighters in Syria, unlike the CIA’s program, which focuses on rebel groups fighting the Syrian military.

While the intelligence alliance is central to the Syria fight and has been important in the war against al-Qaida, a constant irritant in U.S.-Saudi relations is how much Saudi citizens continue to support terrorist groups, analysts said.

“The more that the argument becomes, ‘We need them as a counterterrorism partner,’ the less persuasive it is,” said William McCants, a former State Department counterterrorism adviser and the author of a book on the Islamic State group. “If this is purely a conversation about counterterrorism cooperation, and if the Saudis are a big part of the problem in creating terrorism in the first place, then how persuasive of an argument is it?”

In the near term, the alliance remains solid, strengthened by a bond between spy masters. Prince Mohammed bin Nayef, the Saudi interior minister who took over the effort to arm the Syrian rebels from Prince Bandar, has known the CIA director, John Brennan, from the time Brennan was the agency’s station chief in Riyadh, the capital, in the 1990s. Former colleagues say the two men remain close, and Prince Mohammed has won friends in Washington, D.C., with his aggressive moves to dismantle terrorist groups such as al-Qaida in the Arabian Peninsula.