A judge following the case said the body of Lokman Slim had four bullets in the head and one in the back, in the first such killing of a known activist in years.
One of the security sources also said Slim, who ran a research center and made films, was shot in the head. The second said Slim's phone was found earlier on the side of a road.
They said the motive was not immediately clear.
Slim, in his late 50s, was a leading Shi'ite voice who spoke against what he saw as Hezbollah's intimidation tactics and accused them of intolerance of other political views.
He was last seen after leaving the house of a poet friend on Wednesday night. His family said he went missing overnight. His wife tweeted that he was not answering his phone.
A relative said they found out about his death from a news alert while at a police station to report his disappearance.
Lebanon's caretaker interior minister told local media Slim died in "a terrifying crime" and pledged to pursue the case, which he called "an assassination."
At the family home in the southern suburbs of Beirut, where Shi'ite Hezbollah has a dominant presence, family members sat in shock. Some wept in silence.
"What a big loss. And they lost a noble enemy too...It's rare for someone to argue with them and live among them with respect," his sister Rasha told reporters on Thursday.
She said he had not spoken of any recent threats and tried to keep his family from worrying.
"Killing is the only language they are fluent in," she said. "I don't know how we will go on with our work...It will be hard."
Slim had made documentaries with his wife and led efforts to build an archive on Lebanon's sectarian 1975-1990 civil war.
His criticism of Hezbollah faced rebuke from supporters of the heavily armed movement, who sometimes called him "an embassy Shi'ite," accusing him of being a tool of the United States.
Washington, which classifies Hezbollah as terrorist, has ramped up sanctions against its officials and allies in Lebanon, part of a pressure campaign against Tehran.
Hezbollah did not immediately respond to a request for comment.
Slim founded a nonprofit to promote civil liberties, which had received a grant under the U.S. Middle East Partnership Initiative and worked with an American think tank, leaked Wikileaks diplomatic cables said in 2008.
In a recent interview on Saudi's al-Hadath TV, Slim said he believed Hezbollah has a role in the port blast that ripped through Beirut in August, killing 200 people and injuring thousands.
In late 2019, Slim said his family home and offices were targeted by people gathering in the garden, chanting slurs and threats. His statement held Hezbollah's leader responsible.
At the time, Slim also said he had received death threats after speaking in a debate at a Beirut camp that was set up as protests against all the country's political leaders swept Lebanon."His murder is a very big loss for Lebanon, for culture," Hazem Saghieh, a well-known Lebanese journalist said. "He was one of a few who only knew how to speak his mind."