Security forces opened fire and mowed down demonstrators after tens of thousands gathered at the capital's main stadium
On September 28, 2009 to protest against the regime led by Moussa Dadis Camara.
Women were raped, hundreds of people were wounded and dozens are still missing.
"At least 13 people have been charged," a judicial source told AFP on condition of anonymity, adding that these were on top of eight people already charged since legal proceedings opened in 2010.
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A source in the Guinean Human Rights Organisation confirmed the special panel of investigating judges had unsealed new charges against 13 people.
The list of defendants and their charges was not immediately available.
Hundreds of victims have given evidence since the inquiry into the massacre opened, according to local and global rights organisations.
The eight already accused include the junta's security, public health and special services ministers and Lieutenant-Colonel Claude Pivi, the former head of presidential security.
He was not at the stadium that day but the judges accuse him of masterminding the deadly crackdown that continued in the following days.
Pivi, who denies the charges, was a leading figure in the junta and he was in charge of presidential security for current leader Alpha Conde at the time he was charged.
Conde's government was initially criticised for not taking sufficient action against the suspected masterminds of the stadium massacre.
In exile in Burkina Faso since 2010, he is expected to give evidence from Ouagadougou and faces also being charged, according to local and international charities.