During the 2008 presidential election, Kennedy ordered that State Department employees in Europe be barred from attending Senator Barack Obama's speech in Berlin on July 24, 2008, to ensure they displayed political neutrality. Kennedy labeled Obama's visit as a partisan political activity.
Kennedy's role in diplomatic security decisions has come under scrutiny from politicians since the terrorist attacks on the U.S. Mission in Benghazi in 2012. Kennedy testified to the House Oversight Committee on October 10, 2012, about the death of Chris Stevens. He testified that, after the October 2011 fall of Gaddafi, the government of Libya was in flux, and that Stevens first arrived in Benghazi "during the height of the revolution", which occurred between February 17 and October 23, 2011, "when the city was the heart of the opposition to Colonel Qadhafi and the rebels there were fighting for their lives." At that time he was Special Representative to the National Transitional Council. Stevens returned to Libya as ambassador in June 2012, and was killed on September 11 of that year. The Republican minority on the Senate Select Committee on Intelligence alleged that Kennedy, as Under Secretary for Management, failed to approve requests for additional security in Benghazi and Tripoli, and failed to implement recommendations regarding high-risk diplomatic posts that had been issued after the bombings of embassies in 1998.
Investigation of the ambassador to Belgium
On June 10, 2013, CBS News reported that a memo from an official in the State Department inspector general's office alleged that the then-current ambassador to Belgium, Howard Gutman, was ditching his security detail to engage prostitutes and underage children , and further alleged that Patrick F. Kennedy had killed the original investigation in order to protect Ambassador Gutman and maybe others. On June 11, 2013, White House Press SecretaryJay Carney confirmed that the allegation regarding Kennedy was under active investigation by an independent inspector general. In October 2014, Gutman was cleared by the investigation and the State Department issued an apology for the allegations.
On October 17, 2016, the FBI released interviews related to the Hillary Clinton email investigation. One of the interviews alleges that Patrick F. Kennedy "pressured" the Federal Bureau of Investigation to declassify an email from Hillary Clinton's private server in exchange for a "quid pro quo" of placing more agents in certain countries. The FBI stated that the email's classification status was re-reviewed and remained unchanged and denied quid pro quo accusations. The State Department called the allegations "inaccurate" and maintained that Kennedy was trying to "understand" the FBI's classification process.