Addressing journalists and members of civil society in Islamabad, Clinton highlighted that the Nuclear Supplier Group has raised a number of questions over any nuclear deal with Pakistan.
"The NSG has posed a series of questions that need to be answered There are clearly reservations. Pakistan knows that. I'm looking forward to the answers to the questions," Clinton said.
Referring Dr A Q Khan's nexus, she said Pakistan has a history of proliferation which cannot be ignored.
"The problem with A Q Khan raises red flags for people around the world, not just in the US, because we can trace the export of nuclear information and material from Pakistan through all kinds of channels to many different countries. That cannot be overlooked or put under the carpet," The Dawn newspaper quoted Clinton as saying.
"Pakistan, right now, is the only country standing in the way of the Conference on Disarmament pursuing something called the Fissile Material Cut Off Treaty," she added.