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WASHINGTON — The Obama administration secretly gave its blessing to arms shipments to Libyan rebels from Qatar last year, but American officials later grew alarmed as evidence grew that Qatar was turning some of the weapons over to Islamic militants, according to United States officials and foreign diplomats.

No evidence has emerged linking the weapons provided by the Qataris during the uprising against Col. Muammar el-Qaddafi to the attack that killed four Americans at the United States diplomatic compound in Benghazi, Libya, in September.

But in the months before, the Obama administration clearly was worried about the consequences of its hidden hand in helping arm Libyan militants, concerns that have not previously been reported. The weapons and money from Qatar strengthened militant groups in Libya, allowing them to become a destabilizing force since the fall of the Qaddafi government.

The experience in Libya has taken on new urgency as the administration considers whether to play a direct role in arming rebels in Syria, where weapons are flowing in from Qatar and other countries.

The Obama administration did not initially raise objections when Qatar began shipping arms to opposition groups in Syria, even if it did not offer encouragement, according to current and former administration officials. But they said the United States has growing concerns that, just as in Libya, the Qataris are equipping some of the wrong militants.

The United States, which had only small numbers of C.I.A. officers in Libya during the tumult of the rebellion, provided little oversight of the arms shipments. Within weeks of endorsing Qatar’s plan to send weapons there in spring 2011, the White House began receiving reports that they were going to Islamic militant groups. They were “more antidemocratic, more hard-line, closer to an extreme version of Islam” than the main rebel alliance in Libya, said a former Defense Department official.

The Qatari assistance to fighters viewed as hostile by the United States demonstrates the Obama administration’s continuing struggles in dealing with the Arab Spring uprisings, as it tries to support popular protest movements while avoiding American military entanglements. Relying on surrogates allows the United States to keep its fingerprints off operations, but also means they may play out in ways that conflict with American interests.

“To do this right, you have to have on-the-ground intelligence and you have to have experience,” said Vali Nasr, a former State Department adviser who is now dean of the Paul H. Nitze School of Advanced International Studies, part of Johns Hopkins University. “If you rely on a country that doesn’t have those things, you are really flying blind. When you have an intermediary, you are going to lose control.”

He said that Qatar would not have gone through with the arms shipments if the United States had resisted them, but other current and former administration officials said Washington had little leverage at times over Qatari officials. “They march to their own drummer,” said a former senior State Department official. The White House and State Department declined to comment.

During the frantic early months of the Libyan rebellion, various players motivated by politics or profit — including an American arms dealer who proposed weapons transfers in an e-mail exchange with a United States emissary later killed in Benghazi — sought to aid those trying to oust Colonel Qaddafi.

But after the White House decided to encourage Qatar — and on a smaller scale, the United Arab Emirates — to ship arms to the Libyans, President Obama complained in April 2011 to the emir of Qatar that his country was not coordinating its actions in Libya with the United States, the American officials said. “The president made the point to the emir that we needed transparency about what Qatar was doing in Libya,” said a former senior administration official who had been briefed on the matter.

About that same time, Mahmoud Jibril, then the prime minister of the Libyan transitional government, expressed frustration to administration officials that the United States was allowing Qatar to arm extremist groups opposed to the new leadership, according to several American officials. They, like nearly a dozen current and former White House, diplomatic, intelligence, military and foreign officials, would speak only on the condition of anonymity for this article.

The administration has never determined where all of the weapons, paid for by Qatar and the United Arab Emirates, went inside Libya, officials said. Qatar is believed to have shipped by air and sea small arms, including machine guns, automatic rifles, and ammunition, for which it has demanded reimbursement from Libya’s new government. Some of the arms since have been moved from Libya to militants with ties to Al Qaeda in Mali, where radical jihadi factions have imposed Shariah law in the northern part of the country, the former Defense Department official said. Others have gone to Syria, according to several American and foreign officials and arms traders.

Although NATO provided air support that proved critical for the Libyan rebels, the Obama administration wanted to avoid getting immersed in a ground war, which officials feared could lead the United States into another quagmire in the Middle East.

As a result, the White House largely relied on Qatar and the United Arab Emirates, two small Persian Gulf states and frequent allies of the United States. Qatar, a tiny nation whose natural gas reserves have made it enormously wealthy, for years has tried to expand its influence in the Arab world. Since 2011, with dictatorships in the Middle East and North Africa coming under siege, Qatar has given arms and money to various opposition and militant groups, chiefly Sunni Islamists, in hopes of cementing alliances with the new governments. Officials from Qatar and the emirates would not comment.

After discussions among members of the National Security Council, the Obama administration backed the arms shipments from both countries, according to two former administration officials briefed on the talks.

American officials say that the United Arab Emirates first approached the Obama administration during the early months of the Libyan uprising, asking for permission to ship American-built weapons that the United States had supplied for the emirates’ use. The administration rejected that request, but instead urged the emirates to ship weapons to Libya that could not be traced to the United States.

“The U.A.E. was asking for clearance to send U.S. weapons,” said one former official. “We told them it’s O.K. to ship other weapons.”

For its part, Qatar supplied weapons made outside the United States, including French- and Russian-designed arms, according to people familiar with the shipments.

But the American support for the arms shipments from Qatar and the emirates could not be completely hidden. NATO air and sea forces around Libya had to be alerted not to interdict the cargo planes and freighters transporting the arms into Libya from Qatar and the emirates, American officials said.

Concerns in Washington soon rose about the groups Qatar was supporting, officials said. A debate over what to do about the weapons shipments dominated at least one meeting of the so-called Deputies Committee, the interagency panel consisting of the second-highest ranking officials in major agencies involved in national security. “There was a lot of concern that the Qatar weapons were going to Islamist groups,” one official recalled.

The Qataris provided weapons, money and training to various rebel groups in Libya. One militia that received aid was controlled by Adel Hakim Belhaj, then leader of the Libyan Islamic Fighting Group, who was held by the C.I.A. in 2004 and is now considered a moderate politician in Libya. It is unclear which other militants received the aid.

“Nobody knew exactly who they were,” said the former defense official. The Qataris, the official added, are “supposedly good allies, but the Islamists they support are not in our interest.”

No evidence has surfaced that any weapons went to Ansar al-Shariah, an extremist group blamed for the Benghazi attack.

The case of Marc Turi, the American arms merchant who had sought to provide weapons to Libya, demonstrates other challenges the United States faced in dealing with Libya. A dealer who lives in both Arizona and Abu Dhabi in the United Arab Emirates, Mr. Turi sells small arms to buyers in the Middle East and Africa, relying primarily on suppliers of Russian-designed weapons in Eastern Europe.

In March 2011, just as the Libyan civil war was intensifying, Mr. Turi realized that Libya could be a lucrative new market, and applied to the State Department for a license to provide weapons to the rebels there, according to e-mails and other documents he has provided. (American citizens are required to obtain United States approval for any international arms sales.)

He also e-mailed J. Christopher Stevens, then the special representative to the Libyan rebel alliance. The diplomat said he would “share” Mr. Turi’s proposal with colleagues in Washington, according to e-mails provided by Mr. Turi. Mr. Stevens, who became the United States ambassador to Libya, was one of the four Americans killed in the Benghazi attack on Sept. 11.

Mr. Turi’s application for a license was rejected in late March 2011. Undeterred, he applied again, this time stating only that he planned to ship arms worth more than $200 million to Qatar. In May 2011, his application was approved. Mr. Turi, in an interview, said that his intent was to get weapons to Qatar and that what “the U.S. government and Qatar allowed from there was between them.”

Two months later, though, his home near Phoenix was raided by agents from the Department of Homeland Security. Administration officials say he remains under investigation in connection with his arms dealings. The Justice Department would not comment.

Mr. Turi said he believed that United States officials had shut down his proposed arms pipeline because he was getting in the way of the Obama administration’s dealings with Qatar. The Qataris, he complained, imposed no controls on who got the weapons. “They just handed them out like candy,” he said.