Saleem Shahzad's body was found on Tuesday two days after he went missing.

Earlier a Human Rights Watch researcher said he had "credible information" that Shahzad was in the custody of Pakistani intelligence.

Pakistan has ordered an immediate inquiry into his kidnapping and murder.

"The United States strongly condemns the abduction and killing of reporter Syed Saleem Shahzad," Ms Clinton said in a statement.

"His work reporting on terrorism and intelligence issues in Pakistan brought to light the troubles extremism poses to Pakistan's stability," she said.

Mrs Clinton also welcomed the investigation into the killing.