A group of 275 women and children became the first to be transported to the safety of the Malkohi refugee camp in Yola in the country's northeast.
They are among the nearly 700 freed in the past week. Officials on Sunday are still registering the 61 women and 214 children, almost all girls.
Many critically malnourished babies and children have been put on intravenous drips in the clinic and 21 have been hospitalized for gunshot wounds and fractured limbs, said a camp official.
The women and children were rescued by the military from the Sambisa Forest, the last stronghold of the Islamic extremists, and had to travel for three days on the open backs of military trucks to reach the safety of the Malkohi Camp.
The Nigerian military said the women and girls were freed when soldiers destroyed more than a dozen insurgent camps.
Babatunde Osotimehin, a UN Population Fund (UNFPA) official in Nigeria, said Monday that the rescued women and girls were being tested for disease and infection, including HIV/AIDS.
"We are supporting all of them with various levels of care to stabilize them" said Osotimehin, Anadolu agency reports.
Former captives held by Boko Haram militants in Nigeria have said describing the horror hostages faced in captivity that some of them were stoned to death as the army came nearer to rescue them.
According to BBC, the women said that the captives were pelted with stones when they refused to run away as the army approached nearer.
Around 300 women and children were rescued and brought to a government camp from the vast Sambisa forest.
The military claims to have rescued over 700 people in the last week in the offensive against the militant group.
The women said that the militants killed men and older boys in front of their families and many women were forced into marriage.