It was Pakistan's internal matter, State Department spokesperson Richard Boucher said on Thursday.
An International Atomic Energy Agency official told CNN that IAEA Director General Mohammad ElBaradei had called Khan's revelations "just the tip of the iceberg".
According to the official, ElBaradei was aware of individuals and companies in at least five countries involved in proliferating nuclear technology.
Separately, former IAEA weapons inspector David Albright urged the US to put pressure on Pakistan to be more open with the agency.
Albright, now president of the Washington-based Institute for Science and International Security, told CNN that the IAEA should be able to interview Khan and other Pakistan scientists involved in the country's nuclear programme.
Khan's confession and subsequent pardon "may be necessary, but it's still a charade", he said.