The government-sponsored commission will investigate 4900 cases of people going missing since Algeria was hit by violence following the cancellation in 1992 of elections the popular Islamic Salvation Front was poised to win.
The NGO Human Rights Watch (HRW), based in New York, has put the figure at over 7000.
Rights groups and victims' families who have campaigned for an independent inquiry will be disappointed by the creation of an Algerian government commission to look into crimes the French-backed regime is itself accused of being complicit in.
Rashid Masaoudi, a dissident Algerian journalist now living in London, told Aljazeera that the kidnappings were part of a counter-insurgency policy, that disguised the military's rounding up and extermination of Muslim intellectuals as infighting within the Islamic community.
“Kidnapping people from the streets or at work was safer for the authorities than having them arrested,” Masaoudi said. “It left no records.”
He also claimed that the bodies of those subsequently killed were buried in unmarked graves in Algiers cemeteries.
While there have been few new cases of state-sponsored disappearances since 2000, no safeguards have been put into place to prevent their recurrence.
A HRW report released in February also accused armed groups that claim to be Islamist of kidnapping thousands of Algerians during the armed strife.
The Algerian authorities have so far failed to investigate the disappearances or to provide families with answers about their fate. None of the missing has returned.
The government is seeking closer relations with the United States, the EU and Israel - with whom they are seeking to normalise relations – as a result they want to put the thorny disappearances question behind them.
The human rights commissioner appointed by Bouteflika has spoken about a possible official apology and compensation to the families, but also amnesty for perpetrators.
While there have been few new cases of state-sponsored disappearances since 2000, no safeguards have been put into place to prevent their recurrence, HRW has said.
At least 100,000 are estimated by the government to have died in the complex conflict between Islamic guerrillas and the military, inflamed by counter-insurgency tactics involving security services disguised as Mujahidin.
Intelligence reports quoted in the French newspaper Le Figaro put the toll at over 400,000.