A Chadian military spokesman said fighting took place on Wednesday about 10 kilometres (six miles) from the town of Malam Fatori, which Niger said was retaken by regional forces fighting the Islamist radicals earlier this week.
"Elements of the Chad-Niger (military alliance) were killed in a pocket of resistance," Colonel Azem Bermandoa Agouna told AFP, giving a toll of nine Chadian deaths.
"After heavy fighting, the armed forces of Chad and Niger totally cleaned up the zone," the spokesman added.
The allied troops killed "more than 100" members of Boko Haram in the fighting, according to a Chadian military statement. Some 16 soldiers were injured in the clashes, it added. Large quantities of equipment were also seized by the soldiers.
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Boko Haram's insurgency, aimed at creating a hardline Islamic state, has led to the deaths of more than 13,000 people in northeast Nigeria since 2009.
When the joint force took Malam Fatori on Tuesday, they were unopposed because Boko Haram fighters had gone, but some of the Islamists remained in the vicinity, Agouna said.
That battle left "many wounded on the Chadian and Nigerien sides", according to a humanitarian relief official, who added that "deaths and arrests" were likely among Boko Haram's ranks.