Several people were also reportedly killed in the militant raids on a number of villages in the Kukawa Local Government area in Borno state, a Boko Haram stronghold.
The remote area has poor mobile phone coverage, and details of the Sunday attacks took days to emerge.
A few survivors travelled to Borno's capital Maiduguri, where they briefed reporters on the latest mass abduction by the insurgents, who are accused of killing more than 10,000 people since 2009.
"At first we thought (the attackers) were soldiers... But when they began shooting at people and setting fire to homes we realised they were Boko Haram," Halima Alhaji Adam, from the Doron Baga village.
Adam said the militants kidnapped roughly 100 young men aged between 15 and 30.
Her account was supported by two other women who also reached Maiduguri as well as a leader of a vigilante force which is helping the military in the counter-insurgency fight.
The hostages "were forced into motorboats and taken into Chad," Adam said.
Another woman who escaped, Fatima Suleiman, said locals feared the hostages would be used as "footsoldiers" by the extremists, who regularly carry out strikes on military and civilian targets in the impoverished area.
Mohammed Gava, the Maiduguri-based vigilante leader, said a number of girls and women were also taken.
A multi-national force made up of troops from Nigeria, Chad and Niger are nominally responsible for security in the area.
The force was formed more than a decade ago -- long before Boko Haram became a threat -- to crack down on cross-border smuggling.
The survivors who spoke to AFP said soldiers from this force deployed to the area after the attacks and clashed with Boko Haram fighters on Wednesday when the insurgents returned.
The troops "gave them a good fight," said Suleiman, adding that about 20 people were rescued from captivity.
Adam and Gava similarly reported the rescue but details were not clear and the military could not be immediately reached for comment.
Boko Haram, which says it wants to create an Islamic state in mainly Muslim northern Nigeria, has been accused of kidnapping hundreds of people in the northeast to use as conscripts, wives and slaves.