A missile fired from an American drone has struck and killed a radical US-born Islamic cleric in Yemen, bringing an end to a controversial, two-year manhunt but reigniting questions over the targeting of a US citizen on foreign soil.

Anwar al-Awlaki, a dual US-Yemeni citizen, has been one of America's top targets in its fight against al-Qaida. His firebrand rhetoric had become renowned on jihadi websites and is thought to have inspired many more followers. With a blog, a Facebook page and numerous YouTube videos of his sermons, he had increasingly been regarded by the US as one of the most dangerous al-Qaida leaders.

President Barack Obama authorised a request to target Awlaki in April last year, making him the first US citizen to be a legal target for assassination in the post-9/11 years. He was one of two US citizens killed in the strike. Samir Khan, US-born editor of Al Qaeda's online jihadist magazine, was also killed in the attack, according to Yemeni officials.

Faced with accusations from critics on Friday afternoon that the administration had authorised an "extra-judicial murder", White House officials sought to justify the strike on Awlaki officials as "self defence."

Obama welcomed the news of Awlaki's death. At a ceremony at the White House to welcome the appointment of a new joint chief of staff for the US military, Obama broke from his prepared schedule to say Awlaki's death was a major blow to America's enemies and condemned him as a dangerous terrorist.

"He repeatedly called on individuals in the United States and around the globe to kill innocent men, women and children to advance a murderous agenda," Obama said.

Awlaki is credited with inspiring or directing at least four plots against the US in recent years, three of which were unsuccessful – a shooting inside the Fort Hood military base, the failed Times Square bombing, the failed underwear bomber, and a parcel bomb hidden inside a printer that also failed to explode inside a passenger jet.

The administration avoided giving details of the strike with experts saying they clearly feared further complicating their complex relations with Yemen. At a White House briefing spokesman Jay Carney dodged questions about the legality of the assassination and details of the US's involvement. Nor would he confirm Khan's death or how the bodies were identified.

Asked if the White House would publish evidence that Awlaki was "operationally involved" in terrorism, Charney said: "Again, this is — the question is — makes us – you know, has embedded within it assumptions about the circumstances of his death that I'm just not going to address."

Awlaki's exact role in al-Qaida in the Arabian Peninsula is much debated by security analysts: some claim he had a senior operational role, others say he had a more informal relationship, and some reports said he was at odds with the established leaders of the group. His key role, both locally and internationally, was as a propagandist and inspiration to potential terrorist operators.

The bespectacled and bushy-bearded cleric usually appeared in videos dressed in traditional Yemeni long robe, headscarf and tribal dagger, but he spoke in conversational American English.

With his native English and grasp of Western culture, Awlaki was able to make the often esoteric worlds of radical Islamist theology and Middle Eastern politics accessible and understable to a new audience in Europe and American, introducing political arguments more familiar to listeners who may have had limited understanding of their professed faith.

Awlaki was also linked to failed plots to target British and European interests, according to security officials. The attempted murder of the MP Stephen Timms was inspired by Awlaki's sermons, and a British Airways employee, Rajib Karim, was convicted in February of plotting attacks against the airline.

Awlaki was born in New Mexico in 1971 to Yemeni parents who took him back to Yemen after early childhood. He returned to the US in 1991 to attend college. US authorities believe he came into contact with at least two of the 9/11 hijackers while giving sermons at a San Diego mosque.

He is believed to have been killed at 9.55am on Friday morning at a site 90 miles (140km) east of Sana'a between the provinces of Marib and al-Jawf in what is believed to have been an air strike.

Few details have been released about the strike – not least because the Obama administration is wary of further destabilising the embattled regime of Yemeni president Ali Abdulla Saleh. But witnesses say that Awlaki was boarding a 2005 Toyota Hilux along with five other supporters when the US drone attack hit the vehicle.

Initial reports suggest that it was the drone was operated by the CIA, working alongside the US joint special operations command team that directed the Osama bin Laden assassination.

The death of Awlaki is the most significant blow to the al-Qaida organisation since Bin Laden was assassinated in May. He was one of the few senior operatives orientated to western ways, and in recent years had become increasingly strident in his calls for Muslims to wage jihad against the US.

The CIA and the US military have used drones to target al-Qaida officials in Yemen and had placed Awlaki near the top of a hit list. Yemeni officials initially said they were not yet sure who had killed him. However, they released details of the killing within several hours of it happening, suggesting that Sana'a was either directly involved or well-briefed by the US.

Perhaps mindful of the difficult circumstances in Yemen, Obama was careful to praise the country's involvement in the strike and stress that Islamic militants have carried out many attacks in Yemen.

"Awlaki and his organization have been directly responsible for the deaths of many Yemeni citizens," he said. "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-Qaida."

In a comment piece for the Guardian, former general Wesley Clark said Alwaki's "death makes his final legacy a proof of the effectiveness of America's active defense against terrorists." Would-be Republican presidential candidate Rick Perry praised Obama and the US military for the death of "American-raised al Qaida leader."

But not all reaction was positive. The campaign to take out Alwaki has been criticised by some as a worrying development where the US government can undertake to kill a US citizen without any form of trial.

Republican presidential candidate, libertarian-leaning congressman Ron Paul, spoke out against the attack. "Nobody knows if he [Awlaki] ever killed anybody," Paul said after a political event in New Hampshire where he is currently campaigning. "If the American people accept this blindly and casually … I think that's sad," he added. Paul is a long-standing critic of American foreign policy and the wars in Iraq and Afghanistan.

The American Civil Liberties Union also condemned the attack. The organisation, which campaigns on legal and human rights issues, put out a strongly-worded statement saying the strike was a clear violation of both US and international law.

"This is a programme under which American citizens far from any battlefield can be executed by their own government without judicial process, and on the basis of standards and evidence that are kept secret not just from the public, but from the courts," said ACLU deputy legal director Jameel Jaffer.

He added: "It is a mistake to invest the president - any president - with the unreviewable power to kill any American whom he deems to present a threat to the country."