Carter met with leading human-rights activists in the Caribbean island nation including blogger Yoani Sanchez and dissidents Osvaldo Paya and Elizardo Sanchez, Fox News reported.
Carter, 86, also met with members of the Group of 75, former prisoners whose 2003 Black Spring prison sentences were commuted last year.
Carter met with a dozen of those freed political prisoners who refused to go into exile in Spain, said Berta Soler, a spokeswoman for the Ladies in White, an organization of the dissidents' wives.
"This is recognition for the peaceful labor of opponents who want only an end to the repression and a government that allows its people to lead their own lives," Soler told El Nuevo Herald.
Carter met Tuesday with Castro in what aides described as a discussion of reforms Castro proposed to lift the island nation's anemic economy.
While Carter aides said the visit was "personal," U.S. officials confirmed he spoke with Secretary of State Hillary Clinton and a senior official at the White House's National Security Council before leaving for Havana.
When asked if he was in Cuba to try to secure the release of imprisoned U.S. citizen Alan Gross, Carter said: "We have spoken to some officials about Mr. Gross. But I am not here to take him out of the country."
Gross, who works for Development Alternatives Inc., recently received a 15-year prison sentence for distributing illegal telecommunications equipment, HavanaTimes.org said. The U.S. State Department said it was humanitarian aid.
Carter's visit drew sharp criticism from two Republican U.S. House members, El Nuevo Herald said.
"Carter should demand the Castro regime allow free and fair elections, freedom of the press, the establishment of political parties and the unconditional release of all political prisoners," Rep. Mario Diaz Balart said.
Rep. Ileana Ros-Lehtinen said Cuban security forces detained several dissidents who protested Monday, two of whom had not been heard from as of Tuesday.