FBI / AP Anas al-Liby

Two days after U.S. Special Forces seized one of the FBI’s most wanted al-Qaeda operatives in broad daylight in Libya’s capital, officials of that oil-rich nation are scrambling to explain what they knew in advance about a major foreign commando raid on their territory—an operation that could well provoke jihadist attacks in Libya and destabilize an already fragile government.

The U.S. operation was audacious: Early on Saturday morning, at least two carloads of armed men ambushed Anas al-Liby, one of the suspected masterminds of the 1998 bombings of U.S. embassies in Nairobi and Dar el-Salaam, which killed more than 200 people. As al-Liby returned from dawn prayers to his home in central Tripoli, the men cut off his black Hyundai sedan with their vehicles, smashed the window, pulled him out of the car and flew him out of Libya—all without the Libyan government’s knowledge or approval, or so the authorities in Tripoli claim.

To the U.S., al-Liby’s capture was a long time coming. At 49, al-Liby, whose real name is Nazih Abdul-Hamed al-Ruqai, was a key computer expert for al-Qaeda, who logged time with Osama bin Laden in Sudan and Afghanistan during the 1990s and whom U.S. officials believe acted as a scout and planner for the organization. In 2000, the U.S. indicted him in absentia and others for the embassy bombings. Pentagon officials said on Sunday that al-Liby was “lawfully detained by the U.S. military in a secure location outside of Libya,” which was assumed by some to be a naval vessel in the Mediterranean. The operation’s stunning success was in stark contrast to a second commando raid before dawn on Saturday. U.S. Navy SEALs had tried to storm a house in southern Somalia, the suspected base of key al-Shabab operatives, when they came under a blaze of gunfire and were forced to withdraw before confirming if their target was dead.

Yet despite the success of the Libya operation, the fallout has already begun—and could deepen Libya’s already unstable security situation and shake its fragile government. On Sunday Libyan officials fumed in an official statement that the arrest was a “kidnapping,” and that they have “been in touch with the U.S. government and have asked for clarification on this matter.” Secretary of State John Kerry refused to say on Sunday whether the U.S. had sought Libya’s approval beforehand. But the statement from Libyan Prime Minister Ali Zeidan’s office insisted the government was caught unawares.

That, say Libya watchers, is not believable. For one thing, relatives of al-Liby who witnessed the raid suggest that there were Libyans were among the armed men. “The people who took my father were Libyan, not Americans,” Abdullah al-Ruqai told Libya’s Nabir TV on Sunday, apparently citing his mother, who watched the incident through the window. “They spoke with Tripoli accents.”

In addition, say analysts, even in a city bristling with weaponry, it seems almost impossible that a contingent of armed men could pull off a complex military operation that required spiriting a local resident out of the country, with no official cooperation. “These were not parachutists. These were people who were on the ground,” says Rami el-Obeidi, former intelligence chief for the Libyan rebels during the 2011 war, speaking to TIME from Tripoli. “It was done without a hiccup, smoothly, without a bullet fired. It is impossible to do this without Libyan approval.”

That leaves the government with a more unsettling question to answer—its ability to control a country dominated by divisive, militant factions. Libya is still fractured among several powerful militia groups, and in Eastern Libya, they have effectively established mini-states that take no orders from the capital—and that succeeded in shutting in much of Libya’s crucial oil production for months this summer. Whether or not Libya approved Saturday’s commando raid, the government could stand to lose big. “It will be widely assumed that either Zeidan gave the U.S. permission, or that he did not, and that Libya is incapable of preventing the U.S. from doing this,” says Issandr el-Amrani, North Africa director for the Brussels-based International Crisis Group, speaking to TIME from Cairo. “The Libyan government is barely in control of Libya. It has no ability to enforce the rule of law, or even establish the control of the Libyan national army on the territory.”

Few in Libya are likely to miss al-Liby, who had a $5 million FBI bounty on his head; indeed, many Libyans seemed unaware that he was in Tripoli. Having received asylum in Britain in the early 1990s, he slipped out of sight after the 1998 embassy bombings, and is believed to have finally made his way home to Tripoli as Muammar Gaddafi’s regime collapsed in 2011. There, he seems to have keep a low profile. He appeared to have no involvement with al-Qaeda-linked operations in Libya, like the attack in 2012 on the U.S. Consulate in Benghazi, which killed four Americans, including U.S. Ambassador Chris Stevens.

Still, his arrest could well inspire retaliatory strikes, with perhaps both Libyan government and U.S. interests as the prime targets. Within hours of al-Liby’s capture on Saturday, gunmen attacked a military post in Bani Walid, about 93 miles south-east of Tripoli, killing 15 soldiers. While Libyan officials have drawn no link to the U.S. raid, the attack underscores the government’s struggle in asserting its authority. “One outcome of this operation is that it will push forces hostile to the government to attack it, on the basis that the government is compromising Libyan sovereignty,” says el-Amrani.

The possibility of more violence seems likely to hasten the decision by Western investors to leave Libya—a process that has accelerated since early summer, when the country’s oil production plummeted after local militia groups, who control security over the oil fields and ports, shut down much of the production and exports, as a way of pressuring Tripoli. Libya’s economy is heavily dependent on oil revenues. And ExxonMobil, Marathon Oil and Shell have all said they are seriously considering ending their Libya contracts. That could involve them selling out as discounted prices, given the instability on the ground. “The interest in Libya as an oil-producing country has definitely decreased,” says Riccardo Fabiani, North Africa expert for the Eurasia Group in London. “The authorities are trying to sweeten the terms and entice international oil companies, but they will have to do much more. The companies need security, and that is something the current government can do little about.” Even with al-Liby now in U.S. custody.