"We do not believe in this new story (on Dr Afridi)," a senior Administration official said, adding that the State Department has sought clarification from Pakistan on this confusing signal coming from the country.
Speaking on condition of anonymity, the official said that he does not agree with the argument that Afridi had links with certain terrorist groups.
The tribal court convicted Shakeel Afridi of maintaining close links with the Lashkar-e-Islam, which operates in Bara and Tirah areas of Khyber Agency, and not for his involvement with the American spy agency, media reports earlier said.
The State Department spokesman, Mark Toner, told reporters the US has sought clarification from Pakistan on this issue.
"We are actually seeking clarity on those latest reports. I'm aware of what you're talking about, so we've raised those with the government of Pakistan," he said.
"It seems to contrast previous reports about his conviction and the basis of it, so we're trying to get clarity," Toner said when asked about the new reason being given by Pakistan for sentencing Afridi.
"I mean you know other than raising it very publicly as we've done via Secretary (of State, Hillary) Clinton and raising it consistently in our meetings with Pakistani government officials," he said.
"It's unclear to me what else we could do for his case, but we certainly take it very seriously, the secretary's very clear in her remarks saying that there's not any basis for holding Afridi," Toner added.