Testing has matched DNA from an unidentified body recovered at the scene of the Oct. 2 battle in South Waziristan to that of a family member of Mr. Khadr, who called himself a Canadian aid worker but who was also alleged to be a key financier of Islamic extremist groups in the region.
Reports that Mr. Khadr had been killed began circulating late last fall, but were not confirmed to Canadian authorities until this week.
His youngest son, Abdul Karim, 14, was wounded in the same military engagement and is now in the custody of Pakistani authorities.
"It has been confirmed," a Pakistani official said when asked about Mr. Khadr's death. The delay was due to the long time it took to conduct the DNA test, he added. The body was so badly damaged that even Mr. Khadr's son was not able to positively identify his father. A second Pakistani official also confirmed the death.
Mr. Khadr was born in Cairo but came to Canada in the 1970s and obtained citizenship. He joined the Ottawa-based Muslim charity Human Concern International (HCI) in the 1980s and began traveling to Pakistan and Afghanistan, ostensibly to help refugees of the Soviet War.
But after he was arrested in 1995 on allegations he had financed the bombing of the Egyptian embassy in Islamabad, the Canadian government stopped funding HCI amid concerns that Mr. Khadr's refugee camps were being used by Islamic fighters waging holy war in Afghanistan.
Confirmation of the death means that of the five male members of the Khadr family, only the eldest son, Abdullah, has not at some point been captured. His sister said she had received letters from Abdullah indicating he was hiding in the mountains near the Afghanistan-Pakistan border. Canadian intelligence reports say he ran an al-Qaeda training camp in Afghanistan.
The youngest son, Abdul Karim, is being held in Rawalpindi, Pakistan, and his brother Omar was captured by U.S. forces in Afghanistan and is now detained at Guantanamo Bay, Cuba. The U.S. military plans to put him on trial for killing an American soldier.
Another brother, Abdurahman, was captured by Northern Alliance forces and taken to Guantanamo Bay, Cuba, where he was held by the U.S. military and released. He returned to Toronto in December and admitted that, at his father's urging, he had taken weapons training at a notorious al-Qaeda camp.
The Khadr family has not yet been officially notified that Mr. Khadr's body has been positively identified. An Islamabad lawyer helping the family said he did not believe Mr. Khadr was dead because Pakistani newspapers at the time had named him as having been captured alive.
"It's not possible," said Hashmat Ali Habib.
"According to the news reports, he's alive, Ahmed Said is alive," said Mr. Habib, who has filed a petition asking the Pakistani supreme court to order government authorities to disclose the whereabouts of Mr. Khadr.
"If Ahmed Said would have died, they would have given a big story like, 'We've caught an associate of Osama.' " He also said the family had not provided a DNA sample to compare with the body, although it is possible the sample was taken from Abdul Karim.
Mr. Khadr was considered by Canadian intelligence to be close to bin Laden and a key player in the Canadian Sunni Islamic extremist movement. He and his family were watched closely by intelligence agents and their phones were bugged. Several members of Islamic terrorist groups caught in Canada were linked to Mr. Khadr.
But to some Muslims, he is considered a heroic figure, a humanitarian who collected money in Canada to help fellow Muslims in a part of the world that has long been neglected.