It will also raise questions among military commanders here who would like the U.S. to use its firepower against the Pakistani Taliban, which attacks domestic targets, and not against militants like Nazir who aren't seen as posing as much of a threat to the state, Munir said.
He added that the risk now for Pakistan is that the remnants of Nazir's group could join ranks with the Pakistani Taliban in its war with the government and army.
Drone strikes have been on the rise during Obama's presidency.
According to the Long War Journal, which tracks drone strikes, there were 35 strikes in Pakistan during 2008, the last year President George W. Bush was in office.
That number shot up to 117 in 2010 and then dropped the 46 last year. The strike that killed Nazir was the first of 2013.
The program has killed a number of top militant commanders over the past year, including al-Qaida's then-No. 2, Abu Yahya al-Libi, who died in a drone strike in June on the Pakistani village of Khassu Khel in North Waziristan.
In August, another missile strike in North Waziristan killed Badruddin Haqqani, who has been described as the day-to-day operations commander of the Haqqani network, which has been blamed by the U.S. for carrying out some of the most high-profile attacks against American and NATO troops in Afghanistan.
Associated Press writers Asif Shahzad and Rebecca Santana in Islamabad contributed to this report.