“You've got the Taliban and Al-Qaida operating in the FATA and these border regions between Afghanistan and Pakistan, and what we haven't seen is the kind of concerted effort to root out those safe havens that would ultimately make our mission successful,” Obama said. He noted that it was “not acceptable for Pakistan or for us to have folks who, with impunity, will kill innocent men, women and children.” Obama said he believed the government in Pakistan “cares deeply about getting control of this situation.”

US officials have expressed concern about a Pakistani court’s decision to release rogue nuclear scientist Abdul Qadeer Khan from house arrest and US special envoy Richard C. Holbrooke is expected to express these concerns in his meetings. State Department spokesman Robert Wood said with regard to Dr Khan “we remain very disappointed at the court’s decision in Pakistan. We believe he remains a potential proliferation risk. We will continue to have discussions with the Pakistani government about AQ Khan, and we’re going to continue to follow this issue very closely.”

The court decision on Friday caught the Obama administration off guard, but the US embassy in Islamabad has since been in touch with the Pakistani government on this issue. Wood said what was important to Washington was that non-proliferation activities remained firm and solid.

“We have to do what we can to make sure that, you know, weapons of mass destruction and other types of weapons that can do harm are not able to proliferate, and that’s what we’re going to be working on,” he said. Wood denied suggestions that the government of Pakistan was trying to blackmail the US.

“They know our concern about AQ Khan, and as I’ve said over and over again, we will continue to make that case, and we want to do what we can to make sure that that network can in no way reestablish itself and continue the activities that it was once undertaking,” he said.

Meanwhile, in an interview with the New York Times, Secretary of State Hillary Rodham Clinton said she had first thought of appointing a special envoy for Pakistan and Afghanistan following a trip to the region in 2007.

“We had a series of meetings in both Afghanistan and Pakistan that illustrated dramatically the breakdown in communications between President Karzai and President Musharraf, between the governments of Pakistan and Afghanistan,” she said.

Clinton said when she returned from her trip she urged then-National Security Adviser Stephen Hadley to appoint an envoy to the region, but her request was not acted upon.

Clinton told the paper that she had asked Obama she wanted to appoint special envoys to manage sensitive foreign policy areas during their first conversation when she was interviewed for the Secretary of State job.

“So when President-elect Obama asked me if I would be Secretary of State, I told him in the very first conversation that I had some ideas if I were to accept the job that I thought would be important to explore, and among those were the idea of immediately moving on someone for the Middle East and someone for Afghanistan and Pakistan. He was positive about the idea. He told me to pursue it, work it up, get back to him,” she said. Clinton said she wanted to nominate two envoys for the Middle East and Afghanistan and Pakistan “as soon as possible.”

Holbrooke’s goals in the region is to deliver a message to Pakistan that “they are endangered as much as we are by the continuation of those operations, and that we've got to work in a regional fashion to root out those safe havens,” Obama said.