Sources have confirmed to Al Jazeera that Haqqani and his son Sirajuddin were not present during the attack, and were most likely in Afghanistan.
The school had been closed after previous attacks in the area. Security sources told Al Jazeera that only three foreigners had been inside, confirming they had been killed.
Witnesses said around 17 bodies were pulled from the rubble of the collapsed houses hit in the strike, 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.
Monday's raid is the fourth suspected cross-border strike in the rugged tribal region by the US in almost a week.
US commandos carried out a brief ground assault in the neighbouring South Waziristan region on Wednesday in what was the first known incursion into Pakistan by US troops since 2001.
Pakistani officials said 20 people, including women and children, had been killed in the attack, which drew a furious response from the government.
A day later, four suspected Taliban fighers were killed and five wounded in a missile attack in North Waziristan, believed to have been launched by a US drone aircraft.
Intelligence officials and witnesses said five people had been killed in another suspected drone attack on Friday but the Pakistan military has denied it.