Mr Brebesh served under former Libyan leader Muammar Gaddafi, who was toppled after a nine-month civil war last year.
The country's interim government is under mounting pressure to prevent the abuse of thousands in custody.
Mr Brebesh was detained on 19 January after being called in for questioning by al-Shuhada Ashura militia in Tripoli, Human Rights Watch quote his son, Ziad, as saying.
A day later, his family heard his body had turned up at a hospital in Zintan, about 100km (60 miles) southwest of the capital, the rights group said.
"Photos of Brebesh's body, seen by Human Rights Watch, show welts, cuts and the apparent removal of toenails, indicating that he was tortured prior to death," the group said in a statement.
The BBC's Jonathan Head in Tripoli says the authorities have promised to investigate and stop the torture, and some prisons have been handed over to the justice ministry.
But it has yet to impose its authority on the powerful militia groups which still control parts of Tripoli, he says.
Mr Brebesh served in the embassy to France from 2004 to 2008 as cultural attache and then acting ambassador. He later moved to the foreign ministry.
At the time of his death, Mr Brebesh was still at the ministry, working as a lawyer.
"I saw his face. There was blood on his nose and mouth. But I didn't see the rest of his body or his face from the other side," Human Rights Watch quoted his son, Mohammad, as saying.