Col Moussa Tiegboro Camara is the most senior official to be charged over the massacre, one of the bloodiest events in the West African country's history.
At least 157 people died when the troops opened fire in a Conakry stadium and 100 women were raped.
The colonel was not taken into custody, the AFP news agency reports.
International rights groups welcomed the indictment of Col Tiegboro Camara, who is a minister in the presidency in charge of fighting drug-trafficking and organised crime.
"Ensuring justice for the 2009 victims and their families would help break the cycle of violence, fear, and impunity that has blighted the lives and hopes of so many Guineans for so many years," Corinne Dufka, senior West Africa researcher for the US-based group Human Rights Watch (HRW), said on Thursday.
A HRW report has implicated Col Tiegboro Camara in the 28 September 2009 massacre - saying that he was in the stadium and in command of soldiers who descended on some 50,000 people protesting against the then-military junta of Moussa Dadis Camara.
Eyewitnesses say people were shot, stabbed, bludgeoned or trampled to death and women raped.
Capt Camara seized power in 2008 on the death of long-time leader Lansana Conte, but went into exile not long after the stadium massacre following an assassination attempt.
His deputy oversaw the handover to civilian rule, with veteran opposition leader Alpha Conde winning elections in 2010.
A minister in Guinea has been charged for his role in the killing of scores of people during a protest in 2009 in the capital against military rule.