Washington (CNN) -- The killings Friday of alleged terrorists cleric Anwar al-Awlaki and computer expert Samir Khan could spark retaliatory attacks against the United States, according to the FBI and the Department of Homeland Security.
The agencies issued a joint intelligence bulletin late Friday that said supporters might seek to portray al-Awlaki as a martyr in a supposed U.S. war against Islam. It says the deaths "could provide motivation for homeland attacks" by "homegrown violent extremists," the type the two men allegedly tried to recruit or inspire.
The bulletin came less than a day after U.S. and Yemeni government officials announced that al-Awlaki -- an American whose fluency with English and technology made him a top terrorist recruiter -- was killed in a U.S. drone strike in Yemen.
"It was a joint U.S. military-intelligence operation," a U.S. official said, adding that the U.S. military helped target al-Awlaki and that manned American military aircraft were flying overhead ready to offer assistance. The drone was operated by the CIA, officials said.
The strike also killed Khan, an American, and two others who were in the same vehicle as al-Awlaki, said another U.S. official who was briefed by the CIA. Khan specialized in computer programming for al Qaeda and produced the terrorist network's English-language online magazine, Inspire.
The CIA and the Joint Special Operations Command had al-Awlaki under surveillance for at least two weeks, but were awaiting an opportunity to kill him without causing civilian casualties or damage, an administration official said. CIA and Joint Special Operations Command (JSOC) personnel and assets, including drones, were used to track him and to assess how to target him. JSOC, which commands the clandestine U.S. military units, "played a key role in developing the targeting information."
The source said U.S. Marine Corps Harrier jets were flying overhead to provide backup firepower if needed. In addition, troops from the JSOC units were on standby to board V-22 helicopters in the region to rescue potential downed pilots or to conduct operations on the ground if needed. But the only ordnance used came from the drone, the official said.
The official also said the mission, codenamed Operation Troy, was similar to the one in May that killed al Qaeda leader Osama bin Laden in that it was commanded by the CIA, with close coordination with JSOC.
U.S. President Barack Obama called al-Awlaki's death a "major blow" to al Qaeda, reeling still from the killing and capture this year of several top leaders, most notably bin Laden.
"His hateful ideology and targeting of innocent civilians has been rejected by the vast majority of Muslims and people of all faiths and he has met his demise because the government and the people of Yemen have joined the international community in a common effort against al Qaeda," Obama said.
He said al Qaeda in the Arabian Peninsula, or AQAP, remains a dangerous but weakened organization. "Working with Yemen and our other allies and partners, we will be determined, we will be deliberate, we will be relentless, we will be resolute in our commitment to destroy terrorist networks that aim to kill Americans," Obama said.
A Yemeni government official told CNN that the killing was the result of a "successful joint intelligence-sharing operation" between Yemen and the United States. The official asked not to be named because he is not authorized to speak to the news media.
"This country is much safer as a result of the loss of Awlaki," Defense Secretary Leon Panetta told reporters in Washington. "As far as the operational elements, I'm not going to speak to those except to say that we've been working with the Yemenis over a long period of time to be able to target Awlaki."
Citing bin Laden's killing in May, Panetta added, "This has been a bad year for terrorists." He said he wanted to congratulate the Yemenis "on their efforts, their intelligence assistance, their operational assistance to get this job done." The U.S.-Yemeni effort in pursuing al-Awlaki "was something that involved a tremendous amount of cooperation between the United States and the Yemenis, and today it paid off," he added.
The United States regarded al-Awlaki, the public face of AQAP, as a terrorist who posed a threat to American homeland security. Western intelligence officials said they believe al-Awlaki was a senior leader of AQAP, one of the world's most active al Qaeda affiliates. It has been linked to the attempt to blow up an airliner over Detroit in December 2009 and a cargo plane plot last year.
"Anwar al-Awlaki didn't need subtitles to indoctrinate," said Sajjan Gohel of the Asia Pacific Foundation, who called al-Awlaki's death significant. "He spoke English, he understood how to impact the Muslim diaspora in the West."
Al-Awlaki was killed about 8 kilometers (5 miles) from the Yemeni town of Khashef, east of the capital, Sanaa, said Mohammed Basha, a spokesman for the Yemeni Embassy in Washington. He said the operation was launched at 9:55 a.m.
The Yemeni government official said Yemeni intelligence had recently located al-Awlaki's hideout in a house in Khashef, in Jawf province, which borders Saudi Arabia.
Tribesmen from neighboring Marib province told CNN that they witnessed an attack Friday and that five people who died were burned beyond recognition, raising questions about how al-Awlaki's body had been identified. The tribesmen also said no security officials were present at the scene.
A relative of al-Awlaki said Friday that the cleric is not dead.
Last year, Al-Awlaki's father filed a lawsuit against Obama, then-CIA chief Panetta and then-Secretary of Defense Robert Gates to prevent the U.S. government from trying to target his son for assassination.
A district court judge threw out the case in December, leaving open the question of whether the government has the right to kill Americans abroad without a trial.
The American Civil Liberties Union said Friday that the killing was part of an American counterterrorism program that "violates both U.S. and international law.
"This is a program under which American citizens far from any battlefield can be executed by their own government without judicial process," said ACLU Deputy Legal Director Jameel Jaffer.
But Rep. C.A. Dutch Ruppersberger, D-Maryland, said al-Awlaki was on a "special list" of individuals attempting to attack the United States that is approved by the National Security Council and the president. Targeting those individuals is legal and legitimate, said Ruppersberger, the ranking member of the House Permanent Select Committee on Intelligence, who was in Yemen two months ago.
He called Khan's death collateral damage: "He just happened to be in the vehicle."
Al-Awlaki was born in Las Cruces, New Mexico, and lived in the United States until the age of 7, when his family returned to Yemen. He returned to the United States in 1991 for college and remained until 2002.
It was during that time that, as an imam in California and Virginia, al-Awlaki preached to and interacted with three of the men who went on to become September 11, 2001, hijackers, according to the 9/11 Commission report. He publicly condemned the attack afterward.
In 2006 and 2007, al-Awlaki spent 18 months in a Yemeni prison on kidnapping charges, but was released without trial. Al-Awlaki said he was imprisoned and held at the request of the United States.
U.S. officials say al-Awlaki helped recruit Umar Farouk AbdulMutallab, the Nigerian man known as the underwear bomber, who was charged with trying to blow up a trans-Atlantic flight as it landed in Detroit on December 25, 2009.
The militant cleric is also said to have exchanged e-mails with accused Fort Hood shooter Maj. Nidal Hasan, who is accused of killing a dozen fellow soldiers and a civilian in a rampage at the Texas Army post.
"If you put it into perspective, bin Laden's death had global ramifications for the transnational terror movement," Gohel said. "Anwar al-Awlaki's death will have equal implications for lone-wolf terrorism."
That's because al-Awlaki was articulate and he understood the Western mindset, Gohel said. He knew his way around the Internet and was skilled in indoctrinating impressionable youth.
Early this year, a Yemeni court sentenced al-Awlaki in absentia to 10 years in prison on charges of inciting to kill foreigners.
Prosecutors charged al-Awlaki and two others with "forming an armed gang" to target foreign officers and law enforcement.
At a U.S. congressional hearing this year, Michael Leiter, director of the National Counterterrorism Center, said, "I actually consider al Qaeda in the Arab Peninsula, with al-Awlaki as a leader within that organization, as probably the most significant threat to the U.S."
According to IntelCenter, which monitors jihadist propaganda, Nasir al-Wuhayshi, who is responsible for expanding AQAP's focus on U.S. attacks, remains in charge of the group and further attempts to conduct attacks are expected.
In support of that goal, al-Awlaki was due to release an article in the next issue of AQAP's Inspire magazine on the justifications for attacking civilians in the West. The group announced the upcoming article -- "Targeting Populations of Countries at War with Muslims" -- this week but did not publish it in its latest edition.
Al-Awlaki narrowly survived a U.S. drone assault in May after he switched vehicles with a fellow jihadi, a senior security official told CNN.
Attorneys for al-Awlaki's father, Dr. Nasser al-Awlaki, tried to persuade U.S. District Court Judge John Bates in Washington to issue an injunction last year preventing the U.S. government from trying to kill al-Awlaki in Yemen.
Bates dismissed the case in December, ruling that Nasser al-Awlaki did not have standing to sue.
In a November hearing, lawyers for the U.S. government declined to confirm that the cleric was on a secret "kill list" or that such a list even existed.
Last year, YouTube removed a number of video clips featuring al-Awlaki that it said incited violence.
Rep. Peter King, chairman of the House Committee on Homeland Security, called al-Awlaki's death a "great success" in the fight against al Qaeda.
"For the past several years, al-Awlaki has been more dangerous even than Osama bin Laden had been," the New York Republican said. "The killing of al-Awlaki is a tremendous tribute to President Obama and the men and women of our intelligence community.
"Despite this vital development today, we must remain as vigilant as ever, knowing that there are more Islamic terrorists who will gladly step forward to backfill this dangerous killer."
Al-Awlaki's death is the latest in a string of losses for al Qaeda.
According to Michael Vickers, the U.S. undersecretary of defense for intelligence, eight of the network's 20 key leaders have been killed this year. He cited the killing of bin Laden in May, the death of al Qaeda second-in-command Atiya Abdul Rahman in August, and the capture this month in Pakistan of Younis Mauritani, a senior planner of operations.
Only al Qaeda's current leader, Ayman al-Zawahiri, remains active among those who were among the top nine terrorists at the time of the 9/11 attacks against the United States in 2001.
But al Qaeda is far from dead, Vickers noted, and still poses a dangerous threat to the United States.
"It maintains a worldwide strength numbering in the low thousands. It has broadened its reach through affiliate organizations" in general, but in particular he mentioned al Qaeda in the Arabian Peninsula, which he said has increased its operating space in Yemen.
A statement from the Dar Al Hijrah Islamic Center in Falls Church, Virginia, said al-Awlaki was a peaceful man while he was imam there and turned militant only after returning to Yemen. The statement condemned his espousal of violence.
"Al-Awlaki will no longer spread his hate speech over the Internet to Muslim youth provoking them to engage in violence against Americans," the statement said.
However, the center also rejected what it called "the use of extra-judicial assassination of any human being and especially an American citizen.'
"We reiterate our commitment to due process under law and justice and are concerned that the alleged drone attack sends the wrong message to law abiding people around the world," it said.
CNN's Mohammed Jamjoom, Barbara Starr, Lesa Jansen and Diane Ruggiero and journalist Hakim Almasmari contributed to this report.