"The ISI has a long-standing relationship with the Haqqani network," said Adm. Mullen. "That doesn't mean everybody in the ISI, but it's there. I also have an understanding that the ISI and Pakmil [Pakistan military] exist to protect their own citizens. And there's a way, there's a way that they have done that [had relations with the Haqqani group] for a long period of time. I believe over time that's got to change."

That statement further angered the establishment here. Many disputed the claim as "negative U.S. propaganda."

The ties between the two countries have been strained for months following the fatal shooting of two Pakistani men by CIA contractor Raymond Davis.

On the U.S. side, there is frustration that the Pakistanis are perceived not to be doing enough to rein in extremists or stop cross-border traffic by militants from Afghanistan. Many groups fighting against U.S. and NATO forces find safe haven in the lawless frontier between the two countries.

In order to strike at those safe havens the U.S. often uses unmanned drones and many Pakistanis are furious about this, as they see it as a breach of their sovereignty.

Just after Admiral Mullen’s visit this week a drone strike struck a meeting in North Waziristan reportedly killing 26. The dead included militants but also reportedly some women and children.

Some political activists here say they will begin blocking the vital NATO supply line into Afghanistan if the drone attacks are not stopped.