Bakiev was the prime minister at the time of the incident on March 17, 2002, in which at least five protesters were shot dead by the security forces in Aksy, in Jalal-Abad province. A sixth protester later died from his wounds.
The commission chairman, Dooronbek Sadyrbaev, said the commission also recommends that then-President Askar Akaev and the current chairman of the Supreme Court, Kurmanbek Osmonov, be brought to justice.
Osmonov was Bakiev's first deputy prime minister at the time of the killings. Amid heavy criticism, Bakiev resigned from the post two months after the tragedy.
The commission suggested that Bakiev, Akaev, and Osmonov should be stripped of their immunity in order to face charges. Bakiev's office today denied his involvement in the Aksy violence.
RFE/RL Kyrgyz Service correspondents in Bishkek reported that during the parliamentary session, Sadyrbaev showed a 30-minute-long video of government leaders in 2002 discussing the Aksy events. The video also shows the government forces shooting at the protesters.
Sadyrbaev -- who is also a film director -- said that he has more video files and documents to prove the involvement of police and other authorities in the protesters' deaths.
"As one can see in this video, former Prime Minister Kurmanbek Bakiev did not resign voluntarily [in 2002]. He was pushed and forced very hard to resign by former President Akaev," Sadyrbaev said. He said that while Bakiev denies any connection to the events in Aksy, his signature appears on documents decreeing the special operations there.
No one has thus far been held responsible for the Aksy shootings. But in March of this year, ahead of the fifth anniversary of the Aksy events, the Prosecutor-General's Office announced that the probe into the events had been reopened.
The decision about the new investigation was made after appeals by human-rights groups and nongovernmental organizations, as well as lawmaker Azimbek Beknazarov.
Beknazarov was the Aksy representative in parliament. In early 2002, Beknazarov was detained on charges of abuse of office for his previous work as a district prosecutor.
However, opposition and human-rights campaigners criticized his detention as a politically motivated move following Beknazarov's harsh criticism of the disputed Kyrgyz-Chinese border settlement agreed to by Akaev's government.
The original demonstrations in Aksy began in support of Beknazarov, with some 10,000 people gathering to demand his release. The peaceful demonstrators were stopped by armed police. They then began throwing stones, and the government forces eventually opened fire, killing and fatally wounding several protesters.
The authorities initially blamed the protesters and the organizers for starting the violence.
The international community criticized the Kyrgyz authorities for using force to disperse the demonstrators.
Many Kyrgyz say the Aksy events prepared the country for the revolutionary 2005 events that resulted in Akaev's downfall.
The parliament is to continue its debate on the report on September 17.