Defence Ministry spokesman Zaher Azimy said the case also raised questions about Pakistan's ability to adequately protect its nuclear weapons.
Bin Laden, architect of the September 11, 2001 attacks on the United States, was killed by a US strike team in a military garrison town about 60 km (35 miles) north of Islamabad on Monday. US lawmakers have demanded a review of aid to Pakistan after the disclosure that bin Laden could have been living in the house, which is not far from Pakistan's main military academy, for five or six years.
"When we talk about the location of the house and a military academy nearby ... at the very least it should be known about the activities inside the house and who is living there," Azimy told a news conference.
"If Pakistan's spy agency was not aware of the house near the academy, it brings the agency under question. If I was a security analyst, I would raise these very important questions."
Pakistan's powerful Inter-Services Intelligence (ISI) spy agency and the army have been conspicuously silent about the raid, which has raised questions about whether they knew all along where bin Laden has been hiding.
The ISI has also been accused of maintaining ties with fighters targeting US troops across the border in Afghanistan. Kabul and Islamabad have long had a difficult relationship. Azimy said the killing of bin Laden also raised broader questions about the ISI and the Pakistan military, including its ability to safeguard its nuclear arsenal.
"If the agency was not aware that the biggest terrorist had been living there for six long years, how can it protect its strategic weapons?" he said.
"How can the world be assured that the strategic and atomic weapons would not be in danger in the future?"
Afghan President Hamid Karzai was far less direct in his first comments about bin Laden's killing on Monday, saying that it proved the global fight against militants was "not in Afghan villages".
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