Weapons and ammunition were also recovered, it said.
The six suspects were killed in the Safsafa area near Tipaza, 70 kilometres (44 miles) west of Algiers, according to the ministry.
Algerians had hoped that a 2005 peace and reconciliation charter would turn the page on a 1991-2002 civil war that cost 200,000 lives.
Three Indian soldiers killed as Pakistan Army retaliates on civilian's killing
But militants groups remain active in some areas, largely targeting security forces.
At least 71 armed militants have been killed by Algerian security forces this year, according to an AFP tally of official figures.
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