Karzai made the comment on Friday at a news conference in the capital, Kabul, but gave no suggestion of where he thinks the al-Qaida leader may be hiding
"God knows where he is. ... We don't know. ... He is not in Afghanistan," he said, without elaborating.
His comment came days after Pakistani Interior Minister Aftab Khan Sherpao said bin Laden is not in Pakistan and could be hiding in southeastern Afghanistan.
US officials have said they believe bin Laden is somewhere in rugged mountains between the two nations.