In a statement
, Nato described Saudi-born Sakhar al-Taifi as the group's second most senior figure in Afghanistan.
He commanded foreign insurgents and directed attacks against coalition and Afghan forces, the statement said.
But Taliban sources in Kunar deny Al-Taifi was killed and claim he left the area three months ago.
Sakhar al-Taifi died in "a precision air strike" in the Watapur district of Kunar province on Sunday night, according to the Nato statement. Another rank-and-file member of al-Qaeda was killed at the same time, it said.
But Taliban spokesman Zabiullah Mujahid told the Afghan Islamic Press news agency that a bombing raid in the area had killed two Afghan Taliban.
"There are no al-Qaeda fighters in Watapur and no foreign national was killed there," he said.
Al-Taifi, who also went by the names of Mustaq and Nasim, arranged for weapons and insurgent fighters to be transported into Afghanistan, Nato says.
He reportedly had strong links to Taliban fighters in the area.
Senior intelligence officials have told the BBC's Bilal Sarwary that al-Taifi had expertise in making roadside bombs and suicide vests, but that he also funded and trained suicide attackers in Kunar.
Al-Taifi replaced the al-Qaeda commander Abu Ikhlas al-Masri who was captured in Afghanistan's volatile Kunar province.
Nato estimates that there are fewer than 100 al-Qaeda operatives in the country. However, the border with Pakistan where the fighters operate is porous, says the BBC's Quentin Sommerville in Kabul.
Troops on the ground often report hearing the voices of Arabic-speaking insurgents over radios - when they do, immediate attacks are launched against those sites, he says.
Kunar has always been known as a crucible of conflict - a haven for millitants in the north-eastern corner of Afghanistan and bordering Pakistan's tribal areas.
Correspondents say it is one of the first ports of call for insurgents crossing the mountain passes from Pakistan.
Among the many  
          documents seized from the compound
 of Osama Bin Laden in Pakistan after he was killed last May was a letter to Atiya Abdul Rahman, al-Qaeda's top operational planner, in which the al-Qaeda leader advised militants to seek refuge in Kunar because of its terrain.
"Kunar is more fortified due to its rougher terrain and many mountains, rivers and trees, and it can accommodate hundreds of the brothers without being spotted by the enemy. This will defend the brothers from the aircraft," he wrote.
One of the most senior al-Qaeda figures in Afghanistan was killed in a weekend air strike, Nato-led forces say.