A religious school founded by Haqqani was at first thought to be the target of the attack near Miran Shah, intelligence officials and Pakistani villagers said.
Kamal Hyder, Al Jazeera's correspondent in Islamabad, said: "We know that the attack targeted a compound about one and a half kilometres from where the madrassa of Jallaluddin is located.
"This was a compound where little girls were also studying in some sort of informal madrassa.
"Of course, it was a few days later that there was speculation that senior al-Qaeda members had been killed."
Sources confirmed to Al Jazeera that Haqqani was not present during the attack, and was probably in Afghanistan.
Witnesses said about 17 bodies were pulled from the rubble of the collapsed houses, and more were expected to be found.
Haqqani is a well-known Afghan leader who served as defence minister during the US-led invasion in 2001.
He is also a veteran of the Afghan war against the Soviet invasion in the 1970s and 1980s.
|Asif Ali Zardari was sworn in as president on Tuesday [EPA]
Kamal said: "It's difficult to understand how three or four of their senior commanders would be present at one location. It’s also difficult to understand why the US has not issued a statement. Whenever there is success, the US is very quick to say they have been able to get their man. So again, there will be doubts raised.
"In the past, we have found that high-priority targets have been 'killed' three to four times over. People are already saying that this is yet another attempt to justify an attack that went wrong.
"Whenever such an attack takes place there is considerable anger in the area.
"So it's very difficult for someone to do a tally of the death toll, notwithstanding that this is a very remote region."
Tayyab Siddiqui, a Pakistan analyst in Islamabad, the Pakistani capital, told Al Jazeera that the reports were highly speculative.
"There is even an element of wishful thinking. The Americans seem to be in a kind of paranoia. They are talking about the structure of al-Qaeda and hierarchy being killed and this keeps increasing by the day.
"In fact, there is a huge trust deficit between Pakistan and the United States.
"Both feel the other is not doing enough. The Pakistan army and political leadership feel there is not adequate appreciation of the suffering and sacrifices that have been made in the fight against 'terror'."
The speculation that al-Qaeda leaders have been killed comes a day after a new president was sworn in for Pakistan. Asif Ali Zardari won the election after Pervez Musharraf stepped down under the threat of impeachment.
"President Musharraf lost his popularity primarily because he was considered toeing the American line. So there is an increasing gulf between the government and the people," Siddiqui said.
"Pakistan thinks with a democratic government there will be rethinking of the policy. In the frontier province more than 300,000 people have been displaced and everyone's asking what this is for. It is going to be a major test for President Zardari."