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.

Nigeria wants mobile phone companies to verify the identity of their customers.
The government says it is concerned unregistered Sim cards are being used by criminal gangs.
The South African company has been in talks with authorities since October when the original fine was imposed.
It said on Thursday it had succeeded in reducing the fine by a third.
The original fine amounted to double MTN's annual profits last year.
Since it was imposed by the Nigerian Communications Commission (NCC), MTN has made a number of senior managerial changes, which included the resignation of the chief executive of its Nigerian unit, Sifiso Dabengwa.
"After further engagements with the Nigerian authorities, the NCC has reduced the imposed fine," MTN said in a statement. It added the fine was now $3.4bn.
MTN has 231 million subscribers in 22 countries across Africa, Asia and the Middle East. However, Nigeria is its biggest market.
In September, the company was named as most admired brand in Africa in the Brand Africa 100 awards, beating Samsung, while it was also awarded the continent's most valuable brand, worth $4.6bn (Â£3bn).
MTN was South Africa's second mobile operator when it was set up in 1994 after the end of apartheid.
It began its expansion across Africa four years later with operations in Rwanda, Uganda and Swaziland.

Lorraine Kirkwood, 37, was last seen with a man as they got on to a bus in the East Dunbartonshire town.
Police had appealed for other passengers to contact them.
One of the most senior al-Qaeda figures in Afghanistan was killed in a weekend air strike, Nato-led forces say.
[NEXT_CONCEPT]
Africa's largest mobile operator, MTN, has succeeded in its bid to reduce a $5.2bn Â£3.4bn) fine imposed by Nigerian authorities for failing to cut off unregistered users.
[NEXT_CONCEPT]
A Kirkintilloch woman reported missing, after last being seen on Saturday night, has been found safe and well.