"We don't have any evidence that Osama is in Pakistan," Interior Minister Aftab Khan Sherpao told reporters.
"It is my assessment that the writ of the government is not so strong in the southern and eastern provinces of Afghanistan. Those are Taliban-dominated areas and there could be a possibility of his presence," he said.
'Al Qaeda regrouping in Afghanistan'
On Monday, Sherpao told the state-run Associated Press of Pakistan news agency that bin Laden's top aide, Ayman al-Zawahri, and the Taliban's fugitive chief, Mullah Mohammed Omar, may also be in southeastern Afghanistan.
"The possibility of Mullah (Mohammed) Omar, Osama bin Laden and his close aide Ayman al-Zawahri hiding in that area cannot be ruled out," Sherpao was quoted as saying in an interview, without elaborating.
Sherpao said al-Zawahri and Omar are not in Pakistan.
CIA chief has 'excellent' idea where Laden is
Sherpao's statement comes a day after Afghanistan Foreign Minister Abdullah Abdullah told retired diplomats and bureaucrats at a function in New Delhi that Osama bin Laden and Mullah Omar were not in Afghanistan.
It's a 25 million dollar (the US reward for Osama's head) question," he said, when asked whether he knew the whereabouts of the Al Qaeda's top leadership. ''I have a perception they are outside Afghanistan."
He also accused "terrorists from across the border" stepping up violence in parts of his country before the Parliamentary elections ''just a few weeks away.''
Pakistan is a key ally of the United States in the war against terrorism and its security forces have captured more than 700 al-Qaeda suspects, including several top figures in the terror network.
More reports from: Pakistan | Afghanistan