Algerian newspapers said soldiers killed 15 fighters, but the reports could not be verified from an independent source.
The soldiers, backed by air power, seized 60 AK-47 rifles, 10 rocket launchers and ammunition in the attack on Saturday in the North African country's southern desert, the newspapers reported.
The Islamist fighters, who have links with weapons smuggling networks across Africa's Sahel region, ambushed a party of customs officials on Friday, shooting dead 13 and wounding 10 others 200km from the country's biggest oil-producing town of Hassi Messaoud.
Saturday's raid took place in the same area, in the province of Ghardaia about 700km southeast of the capital, Algiers.
One customs agent was reported missing after Friday's ambush, suspected to have been carried out by members of the Salafist Group for Preaching and Combat (GSPC).
The army offensive is still going on in the region, where security forces have intercepted convoys carrying weapons from neighbouring Mali and Niger, El Watan newspaper, usually well-informed on security matters, quoted security sources as saying.
Eighteen fighters of the GSPC are surrounded by the government forces, the Liberte daily said.
An Islamist uprising broke out in
1992 when polls were cancelled
The authorities, who do not usually speak publicly on security matters, were not immediately available for comment.
Friday's ambush was the worst attack since the government last month started implementing an amnesty aimed at bringing peace following years of violence that killed 200,000 people.
The peace move gives rebels still fighting six months to surrender provided they were not involved in massacres, rapes and bombings of public places.
About 800 rebels are still active, the authorities said. Several fighters have surrendered in the past days, according to media reports.
An Islamist uprising broke out in 1992 when the authorities cancelled legislative elections a now-banned Islamic party was poised to win. They had feared an Iranian-style revolution.