The head of al-Qaeda in Pakistan, who trained operatives for attacks in Europe, has been killed by an American missile strike.

Usama al-Kini died on New Year’s Day along with his deputy, Sheikh Ahmed Salim Swedan, after Hellfire missiles were fired from a CIA-controlled unmanned Predator drone at their hideout in the South Waziristan tribal region of Pakistan. Both men were Kenyan nationals.

Their deaths, coming after a dozen or so top members of the organisation were killed by Predators in the past 18 months, have underlined the accuracy of the intelligence now available to the US.

Although the airstrikes have caused protests in Pakistan, intelligence exchanges between Islamabad and the CIA appear to have greatly improved since the sacking in September of Lieutenant-General Nadeem Taj, the head of the Pakistani Inter-Services Intelligence (ISI) agency.

He was replaced by Lieutenant-General Ahmed Shujaa Pasha, who was in charge of military operations and had launched offensives against militants in the tribal regions. General Pasha is close to General Ashfaq Kayani, Pakistan’s army chief, who has taken a stronger hold over the ISI, which in the past enjoyed significant autonomy.

The latest Predator strikes against al-Qaeda have eliminated two members who have long been high on the CIA’s list of terrorist targets. They were also on the FBI’s most-wanted list, each with a bounty of $5 million for their capture. Al-Kini was suspected of being responsible for the bomb attack on the Marriott hotel in Islamabad in September, which killed 55 people.

Both men were linked to a number of recent suicide attacks in Pakistan and were also suspected of masterminding the bombings of American embassies in Kenya and Tanzania in 1998.

The Predator strike took place near the town of Karikot in South Waziristan. The building targeted by the Predator, which is controlled from a US Air Force base at Creech in Nevada, was being used for explosives training. Last week The Times revealed that al-Qaeda had been forced to carry out training in “class-rooms” rather than outside camps because of the threat posed by the Predators.

Al-Kini was indicted in the US for the 1998 attacks. He became al-Qaeda’s chief of operations in Pakistan in 2007. He was believed to have trained operatives to travel to the US and Europe. A Pakistani security official said: “Al-Kini was a key link between al-Qaeda and Pakistani militants. His death will be a serious blow to al-Qaeda.”

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