The US contractor Blackwater is operating in Pakistan at a secret CIA airfield used for launching drone attacks, according to a former US official, despite repeated government denials that the company is in the country.

The official, who had direct knowledge of the operation, said that employees with Blackwater, now renamed Xe Services, patrol the area round the Shamsi airbase in Baluchistan province.

He also confirmed that Blackwater employees help to load laser-guided Hellfire missiles on to CIA-operated drones that target al-Qaida members suspected of hiding in the Afghanistan-Pakistan border regions, confirming information that surfaced in the US media in the summer.

The secretive base at Shamsi is a key element in the CIA co-ordinated missile strikes that have hit more than 40 targets in the past year. Officials in Washington said that a drone attack on Wednesday killed a senior al-Qaida figure. The officials declined to name the individual, other than to say it was not Osama bin Laden. It is the first time in almost a year that the US has claimed to have successfully targeted a senior al-Qaida figure.

The controversy over Blackwater stems mainly from its work in Iraq and Afghanistan that raised questions about the US use of private contractors in war zones. Several cases against the company are pending in US courts over violent incidents, including a 2007 Baghdad shooting spree.

The New York Times reported today that links between Blackwater and the CIA in Iraq and Afghanistan have been closer than has yet been disclosed, with Blackwater staff participating in clandestine CIA raids against suspected insurgents.

The US and Pakistan governments, as well as Xe, deny the company operates in Pakistan.

Blackwater is a particularly emotive issue in Pakistan, where the company's name, along with the drone strikes, have become lightning rods for anti-American sentiment. Television stations have run images of alleged "Blackwater houses" in Islamabad, while some newspapers regularly run stories accusing US officials and respected journalists of being Blackwater operatives.

US diplomats say the stories are mostly incorrect, and the Pakistani media has confused American contractors from other companies and aid workers with Blackwater employees. Pakistan's interior minister, Rehman Malik, offered to resign if Blackwater was proved to be in Pakistan.

But there is growing evidence to suggest that Blackwater is working in Pakistan. A serving US official said that Blackwater had a contract to manage the construction of a training facility for the paramilitary Frontier Corps, just outside Peshawar, this year. But most of the work on the project, the official said, was done by Pakistani sub-contractors.

Blackwater rebranded itself Xe after the shooting in a Baghdad square that left 17 Iraqis dead. The CIA director Leon Panetta earlier this year ordered that many contracts with Blackwater be terminated. A Congressional committee is investigating links between Blackwater and the intelligence services. Xe, in a statement, denied that Blackwater was ever under contract to participate in covert raids with the CIA or special forces in Iraq, Afghanistan or anywhere else.

In a separate development, five young Americans detained in Pakistan over alleged terrorist links will probably be deported, Javed Islam, a police chief, said. They had not been charged.

The US authorities have not yet said what action, if any, they will take when the five return. The five, aged between 19 and 25, are alleged to have made contact with militant groups. News of their arrest has renewed US fears on homegrown terrorists. The five all attended a mosque in Alexandria, Virginia, run by the Islamic Circle of North America.