Yankuba Badjie headed the National Intelligence Agency, which rights groups say carried out arbitrary detentions, forced disappearances and torture during ousted strongman Yahya Jammeh's 22-year rule.
Badjie and the eight others pleaded not guilty to the charges by prosecutors yesterday.
The nine men, including the NIA's former director of operations, Saikou Omar Jeng, denied killing opposition figure Solo Sandeng of the main opposition UDP.
Sandeng was arrested on April 14 last year while leading a demonstration for political reform and died in custody at the NIA headquarters.
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UDP chief Ousainou Darboe, a human rights lawyer, and other party leaders, were subsequently arrested.
In July, Darboe and about 30 other co-accused were sentenced to three years in jail for six offences related to the April protest.
But on December 5, 2016, Darboe was freed on bail with 18 others, days after Jammeh lost the vote to outsider Adama Barrow.
Barrow has promised to reform the NIA -- changing its name, replacing its chief and promising training for staff whose work would be limited to "intelligence gathering, analysis and advice to the relevant arms of government".