"Actually, contrary to public perception, CIA and ISI are the best of partners," Haqqani told the MSNBC news channel in an interview.
"Just as there are people who don't want to believe the birth certificate even if it exists, similarly, there are people who don't want to believe that the ISI is a partner of the CIA. And that causes a lot of problems," Haqqani said referring to the controversy surrounding the birth certificate of President Barack Obama.
"The truth is that, in the last few months, we have really worked at bridging the gap. Last week, Pakistan's Foreign Secretary was in town. We had intense meetings.
Ambassador Grossman, President Obama's new special representative for Afghanistan and Pakistan, is headed to Pakistan," he said.
Haqqani said the CIA and the ISI have already worked out an arrangement whereby they will be able to have measures that will enable each other to trust each other on certain specifics.
"We have overcome the rough patch. The important thing is Pakistan needs the US, and the US needs Pakistan. We are allies. We are partners, and we will work together," Haqqani said.
The Pakistani Ambassador down played the recent statement by Admiral Mike Mullen, Chairman of the Joint Chiefs of Staff, that elements in ISI has links with the terrorist Haqqani network.
"What he did was he actually asserted an intelligence assessment over which Pakistan and America have disagreed over a long time. Now, it is something that is a subject of an ongoing discussion between us. We intend to clear it up. We want Afghanistan to be a stable state in our neighborhood. We want the United States to succeed in Afghanistan, and we intend to work with the US," Haqqani said.
"There's a long history here. The new democratic government that took over in 2008 has come a long way in building a strategic partnership. It will take us a little more time to overcome the burden of history," Haqqani said.