Clinton said the talks are necessary and she credited President Barack Obama's aggressive military strategy for making them possible, The Washington Post reported.
"Only now are we beginning to see the kind of outreach that evidences a willingness to discuss the future," Clinton said Thursday.
The talks so far have been "very preliminary," she said.
The Post said U.S. officials had three meetings with Mohammed Tayeb al-Agha, an aide to Taliban leader Mohammad Omar.
The officials said they were not sure how future talks would proceed. They said the Taliban complied with an arrangement made by the two sides at their third meeting by posting a coded acknowledgment of the talks, the Post reported.
Afghan President Hamid Karzai has talked about the meetings but U.S. officials told the Post his government has not participated in them because the Taliban had said they wanted to speak to the United States directly.
Among the Taliban's demands is the setting up of an independent political office outside of Afghanistan, likely in Qatar, the report said.
The initial meetings were in Qatar and Germany.