For several years, the CIA has been conducting a secret drone program in Pakistan, targeting Islamist militants in the mountainous region near the border with Afghanistan. The Pakistani government has secretly allowed the program while publicly protesting it, because the Pakistani public is mostly against it. In 2011, Pakistani officials push back against the program due to the growing number of strikes and an increasing public backlash.
In June 2011, the Wall Street Journal reports that there is a debate about the scale of the program inside the US government. State Department and military officials argue that the CIA needs to be more selective with their strikes. Also, for the first time, State Department officials are given a say. The CIA begins notifying US ambassador to Pakistan Cameron Munter about planned drone strikes, and this information gets passed up the State Department to Clinton and other top officials. The department then gets to concur or not concur with the strike.
For the rest of Clinton’s tenure until February 2013, the department objects to a planned strike only once or twice. But the strikes will often be discussed by Clinton and other State Department officials in unsecured email channels, and this will later be a focus of the FBI’s Clinton investigation. (The Wall Street Journal, 6/9/2016) (The Wall Street Journal, 6/4/2011)