In an interview with the newspaper, the outgoing chairman of the U.S. Joint Chiefs of Staff also discussed his recent remark at a Senate hearing that the violent Haqqani Network is a "veritable arm" of Pakistan's spy agency, the Inter-Services Intelligence directorate, or ISI.
On long-term strategic partnership with Pakistan, of which he has been a strong supporter, the admiral said: "I certainly think the case for it has been made much more difficult by the series of events that we have been through …"
However, he added: "My view is long term, we need to have that strategic relationship. But it's long-term, and it is longer term now than it was just a few months ago."
Mullen, who made numerous trips to Pakistan and Afghanistan as the top U.S. military leader, told the Journal he has been the "Pakistan's best friend."
On what caused him to chastise Pakistan over the Haqqani Network issue, Mullen cited a series of recent attacks in Afghanistan including the Sept. 13 attack on the U.S. Embassy in Kabul and "the links to Haqqani with respect to all of those specific attacks, and the strategic support that the ISI has given over a long time (to) Haqqani."
He said he doesn't believe the Pakistani military or the ISI have complete control of Haqqani but "it's very clear that they have supported them over time."
"There's a ratcheted-up intensity. I'm losing people, and I'm just not going to stand for that. … I have been Pakistan's best friend: What does it say when I'm at that point? What does it say about where we are?"