"(Defence) Secretary (Leon) Panetta spoke to our concern about how these two organisations operate and any relationship that they may have with Pakistan, which is a subject that we talk about with Pakistan," State Department spokesperson Victoria Nuland told reporters.
She, however, said this was a "different issue" than a State being "a sponsor of terrorism itself".
Nuland's comments come shortly after Panetta acknowledged that Pakistan keeps ties with anti-India terror group LeT.
Asked if it was her understanding that what Panetta was meaning to say was that the Pakistani government has relationships with these two networks, Nuland said "No".
"We believe it is in our interest and it's in the interest of Pakistan that we continue to strengthen our cooperation and collaboration," she said.
Nuland said there was no secret to anybody that US has a robust dialogue with Pakistan on counter terrorism issues, and it continues to try to strengthen their approach and collaborate "as much as we can".
"Obviously, these two organisations that Secretary Panetta spoke about are on the list of subjects that we talk about together. But beyond that, I don't think I'm going to get into the substance," she said.