"We have conveyed to the US that you will lose an ally. You cannot afford to alienate Pakistan, you cannot afford to alienate the Pakistani people," she said, adding "If they are choosing to do so, it will be at their own cost."
Khar's remarks came a day after US military chief Admiral Mike Mullen accused the ISI of supporting the Haqqani network in carrying out a string of deadly terror attacks, including an assault on the US Embassy in Kabul on September 13.
He said the Haqqani network, a powerful faction of the Taliban, was a "veritable arm" of Pakistan's spy agency.
Mullen's tough words marked the first time a US official had linked ISI directly to these terror groups, signaling a significant change in the American approach to Islamabad.
The Pakistan Foreign Minister, who is in New York to attend the UN General Assembly meeting, told Geo News channel that though militants based in Afghanistan had carried out cross-border attacks on Pakistan, Islamabad had not resorted to a blame game even though US forces are responsible for security on the Afghan side.
It is in the interest of both Pakistan and the US to retain their relationship, Khar said. "So, if it is not a relationship of complete equals, them being a superpower and us not, but it is (a relationship) of sovereign equals." Both countries need each other and Pakistan wants its relationship with the US to remain intact, she said. But Pakistan's sovereignty must be respected by the US, she added.