More than 150 people were killed when security forces opened fire on thousands of anti-government protesters at the capital’s main stadium.
Women there were raped and dozens of people were never seen again.
An inquiry was launched in 2010, after Capt Camara was ousted and fled to Burkina Faso, where he still lives.
Capt Camara was indicted by magistrates who came from Guinea on Wednesday to question him about his alleged involvement in the September 2009 massacre, his lawyer Jean-Baptiste Jocamey Haba told AFP by telephone from Ouagadougou, the capital of Burkina Faso.
Capt Camara’s Patriotic Front for Democracy and Development said the interrogation was a “purely political” reaction to his announcement that he intended to run for president in elections due in October.
Hundreds of victims have given evidence to the massacre inquiry, local and international rights organisations say.
Capt Camara seized power in 2008 when long-time leader Lansana Conte died.
Thirteen other members of the military government are facing charges in relation the massacre, in addition to eight people already indicted.