One of the women told the AFP news agency that Boko Haram members had ushered a group of civilians into waiting buses three days earlier and threatened to kill them if they refused.
The woman, a theology student, said: "We asked questions about our mission but we did not get any answers.
"We were only told that we would continue our studies in Maiduguri and be brought back later."
Boko Haram, which means "Western education is prohibited" in the local Hausa dialect, has called for the enforcement of sharia, or Islamic law, in the country, including among non-Muslims.
Nigerian authorities said the group's leader, Mohammed Yusuf, was killed in a shootout on Thursday by security forces as he attempted to flee his compound in Maiduguri.
But Al Jazeera's Yvonne Ndege, reporting from Maiduguri, said there were still questions about whether Yusuf is alive or dead.
"The military say he was shot dead at the compound by the army, but promises to show his remains to Al Jazeera have not been delivered on, leading many to wonder whether they got the right man," she said.
"The authorities also deny rumours he was killed in custody by police as human rights organisations allege."
About 600 people were killed in days of fighting that began on Sunday in the northern Bauchi state, with Boko Haram fighters attacking police stations, before the clashes spilled over into neighbouring states.
Nigeria's 140 million people are nearly evenly divided between Christians, who dominate the south, and the primarily northern-based Muslims.
Islamic law was implemented in 12 northern states after Nigeria returned to civilian rule in 1999 following years of military rule.