Kongantiev's spokesman Toktogul Kakchekeev told RFE/RL's Kyrgyz Service that the probe will be completed "in December."
"It would be [unreasonable] to ask us to finish within one month or two weeks because the investigation has been going on at a slow pace for many years now," he said.
Six police officers and regional prosecutors were dismissed and charged over the Aksy shootings. They claimed they had received orders to fire on the protesters and were subsequently acquitted.
Bakiev promised to prosecute all those responsible for the shootings when he became president last year.
Bakiev was prime minister at the time of the Aksy incident.