The total was announced on Tuesday at a news conference for journalists by Ahmed Ouyahia, the Algerian prime minister, who did not say who he believed was responsible for the other 180,000 deaths, mostly civilians, resulting from the conflict.
The authorities normally blame the rebels for the bloodshed of the period.
The North African country was plunged into conflict when the authorities cancelled a legislative election that a now-banned Islamic party was poised to win in 1992.
As part of an attempt to put a final end to the conflict, the authorities started releasing jailed militants this month under an amnesty, which also provides for compensation for victims of the violence.
A total of 2,629 militants are due to be released.
The so-called national reconciliation process is being closely watched throughout north Africa, an energy-rich region whose stability was threatened by the turmoil in Algeria.
State radio quoted Ouyahia as saying 8,000 people were missing, compared with the previous official estimate of 6,146.
The peace drive gives rebels still fighting six months to surrender.
Noureddine Zerhouni, the interior minister, said on Saturday that about 100 rebels have given themselves up but about 800 are still active
Ouyahia said the government would continue its crackdown until all rebels surrendered, and reiterated that the authorities were not ready to lift a 15-year-old state of emergency.
"The state will continue to fight against terrorism with more ferocity," state radio quoted him as saying.