Abu Zeid Omar Dorda is also charged with arming his ethnic group
The first senior official from the former Libyan regime has been charged in court in connection with the conflict that toppled Muammar Gaddafi.
Abu Zeid Omar Dorda, who was the head of external intelligence, appeared in the Tripoli court behind a metal cage.
He denied all six charges, which included ordering the fatal shooting of protesters last year.
The case has been adjourned until 26 June as his lawyer asked for more time to review the case.
Mr Dorda was arrested in September 2011, the month before Col Gaddafi was killed.
The BBC's Rana Jawad in the capital, Tripoli, says his trial is seen as a test case for Libya's judiciary and its capacity to deal with high-profile cases.
Mr Dorda is charged with "mobilising security forces to fire bullets at the heads and chests of civilians" and "preventing, through the use of force and intimidation, the staging of peaceful protests", the Libya's state-run news agency Wal reports.
He is also charged with arming his ethnic group with the purpose of inciting civil strife during Libya's seven-month rebellion last year.
Mr Dorda arrived in court wearing a blue prison uniform - looking slightly weary and using crutches to walk, our correspondent says.
His doctor told the BBC the former head of foreign intelligence was recovering from a broken hip.
His younger brother, Abdullah, was in the court house and told the BBC that he was confident of his brother's innocence, adding that the family was coping with a stressful situation.
"All these things they're saying about him are not true... my brother is one of the Libyan people who looks out for his country, for its people and its safety," he said.
Defence lawyer, Daw al-Mansouri, told reporters that he had faith that his client would receive a fair trial.
Mr Dorda, 68, once served as Libya's prime minister and as an envoy to the UN.
He took over as external intelligence chief in 2009 from Moussa Koussa, the foreign minister who defected in March 2011 from the regime and fled Libya, initially to the UK.
Mr Dorda was one of Gaddafi's most loyal supporters - even calling in to state TV in April last year to deny reports that he was defecting.
"It is impossible for Abu Zeid Dorda to think, not only when awake but even when dreaming, of leaving Libya or the Libyan people or the revolution, or betraying its leader Muammar al-Gaddafi," he said.
"I am in Libya and am going to stay in it, and I am steadfast in the victorious revolution's trench."
Two other key figures in former regime are wanted for alleged war crimes by the International Criminal Court (ICC) - Gaddafi's son Saif al-Islam, who is in custody in Libya, and his brother-in-law Abdullah al-Senussi, the former head of military intelligence.
Libya has insisted they should both be tried by a Libyan court.
Mr Senussi, who was captured in Mauritania last November, has been charged with illegally entering the West African country.