"The United States strongly condemns the abduction and killing of reporter Syed Saleem Shahzad," she 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.
Clinton said Washington welcomed Pakistan's launch of an investigation into the killing.
Shahzad, 40, who worked for an Italian news agency and an online news site registered in Hong Kong, went missing on Sunday. His body was found 150 kilometres (93 miles) southeast of Islamabad.
He disappeared two days after writing in an investigative report in Asia Times Online that Al-Qaeda carried out last week's attack on a naval air base to avenge the arrest of naval officials suspected of having links to the group.
The May 22 attack took 17 hours to repel, and officials said six militants destroyed two US-made surveillance aircraft and killed 10 security personnel.
The country's umbrella Taliban faction claimed responsibility, saying the attack was carried out to avenge the US killing of Osama bin Laden, which reopened questions about complicity with Al-Qaeda within the military.
Ali Dayan Hasan, senior South Asia researcher at Human Rights Watch, said Shahzad had complained about being threatened by Pakistan's Inter-Services Intelligence (ISI) agency, long accused of having ties to Islamist militants.
Pakistani Prime Minister Yousuf Raza Gilani ordered an inquiry into the kidnapping and murder, pledging that the culprits would be "brought to book".
US-Pakistani relations have been tense in recent weeks following the killing of bin Laden in Pakistan by US commandos in a raid carried out without Islamabad's knowledge.