Scores of Boko Haram militants stormed the Malari village around 8:00 pm (local time) and whisked away the males, aged between 10 and 23, into the nearby Sambisa forest, believed to be one of the Islamists' major bases.
The news of the abductions came out only days later, after residents who fled the village arrived in the state capital Maiduguri late yesterday.
"They came in pick-up trucks armed with guns and gathered all the men in the village outside the home of the village chief where they preached to us before singling out 40 of our boys and taking them away," Bulama Muhammad told AFP.
"My two sons and three nephews were among those taken away by the Boko Haram gunmen and we believe they are going to use them as conscripts," Muhammad said.
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"When we heard of the kidnap of 40 boys in Malari by Boko Haram we decided to leave because we could be the next target," said Alaramma Babagoni, who fled from the nearby village of Mulgwi.
"Boko Haram has been abducting young men from villages in the area because we are close to their stronghold in Sambisa forest," he said.
Residents of Malari and nearby villages fled, fearing further attacks and abductions.
Boko Haram has recently been seizing young men during raids on area villages to use as foot soldiers in its uprising aimed at establishing an Islamic state in northern Nigeria, residents said.
Suspected Boko Haram gunmen launched a deadly raid Tuesday on Kautikari village near Chibok, torched several buildings and killed as many as 15 people, according to witnesses. There was no toll available from an official source on the raid.
Boko Haram is still holding in captivity more than 200 schoolgirls it abducted from their school in Chibok in Borno state last April.