The attack happened in the town of Gajiram, about 80 kilometres by road north of the Borno state capital, Maiduguri, on Wednesday afternoon.
A military source in Maiduguri and a civilian vigilante, Babakura Kolo, both told AFP yesterday that the fighting lasted for about two hours and that three soldiers were killed.
But Kolo said today that the toll was had risen and that it was "now seven, including one lieutenant, and six rank and file.
The security source said three militants were also killed and troops were combing the area to find other rebel fighters.
AFP contacted the military for comment but there was no immediate response.
Fighters loyal to Abu Musab Al-Barnawi were suspected of carrying out the attack, said Kolo.
The Islamic State group, to which Boko Haram is affiliated, announced that Barnawi was leader last year.
He split from the faction following long-time Boko Haram leader Abubakar Shekau in opposition at his indiscriminate attacks on civilians.
According to the security source, the insurgents went door to door collecting recently distributed food aid for residents.
Kolo said vigilantes had been told by arrested Boko Haram suspects that they sourced most of their food from Gajiram and Monguno, a garrison town 60 kilometres away.
Nigeria's government wants the hundreds of thousands of displaced people staying in camps and host communities to return to their homes as soon as the military makes areas safe again.
"Some displaced people were returning to their villages in the area to harvest their abandoned cornfields when they were intercepted by Boko Haram," said Kolo.
"They killed some and took away others," he said, without specifying a death toll.
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