Pakistan's army has long been seen as the most effective institution in an unstable country where civilian leaders are seen as too inept and corrupt to handle any crisis.
Now political parties and ordinary Pakistanis are asking unusually tough questions about how the assault could have taken place in a garrison town without the knowledge of the army.
The United States wants to know if Pakistan -- recipient of billions of dollars in U.S. military aid -- knew that bin Laden was living comfortably in the city of Abbottabad not far from the capital.
For some Pakistanis, the burning, and embarrassing issue, is how the assault in a city beside a Pakistani military academy took place while the army was kept in the dark.
"Every Pakistani wants to know how come the borders of an independent and sovereign country were violated, an attack was carried out, people killed and then the foreign attackers fled safely, and our agencies remained unaware," said Altaf Hussain, of the Muttahida Qaumi Movement, a key government ally.
Pakistan has welcomed bin Laden's death, but its foreign ministry expressed "deep concerns" about the raid, which it called an "unauthorised unilateral action".
The CIA said it kept Pakistan out of the loop because it feared bin Laden would be tipped off, highlighting the depth of mistrust between the two supposed allies.
U.S. helicopters carrying the commandos used radar "blind spots" in the hilly terrain along the Afghan border to enter Pakistani airspace undetected in the early hours of Monday.
"There is not just confusion that prevails in Pakistan, but also a national depression at the loss of national dignity and self-esteem as well as sovereignty," cricketer-turned-politican Imran Khan, wrote in Britain's Independent newspaper.
The Pakistani media, as well as ordinary people, are not only decrying what they say is a breach of sovereignty, but are also worried about the safety of the country's nuclear weapons.
"The biggest question is where do we stand now? We had the belief that our defence was impenetrable, but look what has happened. Such a massive intrusion and it went undetected," said prominent television political anchor Kamran Khan.
"After such a lapse, what is the guarantee that our strategic assets and security installations are safe? There is anger all around, and this is a cause where anger should be built," he said.
Pakistan spends a huge chunk of its budget every year on defence, thanks to its old rivalry with neighbour India and the war against homegrown Taliban militants.
The military, though often criticised for its role in politics, is largely respected.
"We have been feeding the military for decades at the cost of our children's future, their education, everything," said Ibrahim Ali, a shopkeeper in a middle class neighbourhood of the city of Karachi.
"But look how capable they are. Tomorrow, the Indians will come and attack us and we will just say that they used technology and exploited the blind spots. It's ridiculous."