WASHINGTON — Days after the Justice Department closed out its criminal investigation of the deaths of two detainees while in the custody of the C.I.A., new information has surfaced calling into question official accounts of the extent of waterboarding by American interrogators.

A new report by the nonprofit group Human Rights Watch, based on documents and interviews in Libya after the fall of its dictator, Col. Muammar el-Qaddafi, includes a detailed description of what appears to be a previously unknown instance of waterboarding by the C.I.A. in Afghanistan nine years ago.

That claim clashes with repeated assertions by current and former agency officials that only three high-level terrorism suspects — none of them Libyans — were waterboarded.

The account documented by Human Rights Watch could not be independently corroborated. But the report’s description of interrogation methods, based on individual interviews with former prisoners who had not sought out the human rights workers, match up with official documents on C.I.A. techniques. It underscores how much is still not known about the United States’ treatment of terrorist suspects during the early years of the Bush administration.