Major general Pranowo was head of the Jakarta military police when soldiers opened fire on Muslim demonstrators in the Tanjung Priok area in 1984, killing at least 14 people.
Rusmanadi, who leads the team of prosecutors, began proceedings on Tuesday by reading the indictments against Pranowo.
Court officials said he faced crimes against humanity charges under a law on human rights issued in 2000.
If convicted, he would face a maximum punishment of life in prison.
The Tanjung Priok trials began on 15 September when Captain Sutrisno Mascung and 10 other soldiers went on trial, accused of firing at the protesters.
The trials are Indonesia's second major attempt to bring soldiers to court for rights' abuses.
Dozens of uniformed soldiers were in court on Tuesday to support the accused, while a large group of people from the massacre victims' families were also present.
During the incident, troops opened fire on Muslim activists gathering in the Tanjung Priok port area to seek the release of four people detained by the military.
The protests took place amid a climate of revolt against the autocratic rule of then-president Suharto.
Indonesia is the world's most
populous Muslim nation
An investigation by the National Commission on Human Rights found that at least 24 people were killed and 54 injured in the shooting spree.
Separate trials over the massacre will later see two other generals in the dock - retired major general Butar Butar, and the current chief of the Kopassus army special forces, Major General Sriyanto Mustrasan.
Rights' activists have alleged the government is not serious about bringing the military to account for the Tanjung Priok case because the then-armed forces commander and Jakarta military chief have not been indicted.
Activists said the trials could have ramifications for the restoration of military aid to Indonesia from the United States.
The US administration halted most military contacts with Indonesia over the 1999 bloodshed in East Timor, and says this would not be restored until soldiers are held to account for abuses.
However, the US was an ardent supporter of the dictatorial Suharto government when the massacre took place.