Suspected Islamic extremists attacked an agricultural college in the dead of night, gunning down dozens of students as they slept in dormitories and torching classrooms.
The gunmen, thought to be members of rebel sect Boko Haram, attacked one hostel, took some students outside before killing them and shot others trying to flee, people at the scene told Reuters.
Boko Haram, which wants to establish an Islamic state in northern Nigeria, has intensified attacks on civilians in recent weeks in revenge for a military offensive against its insurgency. Several schools, seen as the focus of Western-style education and culture, have been targeted.
"They started gathering students into groups outside, then they opened fire and killed one group and then moved onto the next group and killed them. It was so terrible," said one surviving student Idris, who would only give his first name.
"They came with guns around 1am and went directly to the male hostel and opened fire on them ... The college is in the bush so the other students were running around helplessly as guns went off and some of them were shot down," said Ahmed Gujunba, a taxi driver who lives by the college.
Bodies were recovered from dormitories, classrooms and outside in the undergrowth on Sunday, a member of staff at the college told Reuters, asking not to be named.
Provost Molima Idi Mato of Yobe State College of Agriculture told The Associated Press that there were no security forces protecting the college. Two weeks ago, the state commissioner for education had begged schools and colleges to reopen and promised they would be guarded by soldiers and police.
Soldiers recovered 42 bodies and transported 18 wounded students to Damaturu Specialist Hospital, 40 kilometers north, said a military intelligence official who insisted on anonymity because he was not authorised to speak to the press.
Two of the wounded later died, said Adamu Usman, a survivor from Gujba who was helping at the hospital.
President Goodluck Jonathan condemned the assault as "the creation of the devil" in a "chat with the media" Sunday night, and questioned the motives of Boko Haram, which wants to impose Islamic law across Nigeria. He said he wondered whether the victims were Muslim or Christian.
Usman said almost all those killed were Muslims, as is the majority of the college's student body.
Jonathan likened the assault to that on Nairobi's premier shopping mall last week, where Islamic extremists from Somalia's al-Shabab movement killed 67 civilians - but only after allowing many Muslims to leave. Boko Haram has said some of its fighters trained with al-Shabab in Somalia.
Boko Haram leader Abubakar Shekau has said in video addresses that his group wants to end democracy in Nigeria and allow education only in Islamic schools. Boko Haram means "Western education is forbidden."
Its uprising poses the biggest security challenge in years to this country. Nigeria is Africa's biggest oil producer and its most populous nation with more than 160 million people - almost equal numbers of which are Muslims and Christians.
Boko Haram militants have killed more than 1,700 people since 2010.
"Sometimes you need courage" to confront such challenges, Jonathan said, accusing the extremists of choosing soft targets to embarrass his government.
Governor Ibrahim Gaidam of Yobe state, where the killings occurred, indicated that the military crackdown is ineffective.
"Although there is (an) increase in troop movement and military hardware deployment in the northeast, people are yet to see the kind of action on the ground that effectively nips criminal and terrorist activities in the bud," he said in a statement.
The extremists rode into the college in two double-cabin pickup all-terrain vehicles and on motorcycles, some dressed in Nigerian military uniforms, a surviving student, Ibrahim Mohammed, told the AP. He said they appeared to know the layout of the college, attacking the four male hostels but avoiding the one hostel reserved for women.
"We ran into the bush, nobody is left in the school now," Mohammed said.
Wailing relatives gathered outside the hospital morgue, where workers laid out bloody bodies in an orderly row on the lawn for family members to identify loved ones.
One body had its fists clenched to the chest in a protective gesture. Another had hands clasped under the chin, as if in prayer. A third had arms raised in surrender.
Provost Idi Mato confirmed the school's other 1,000 enrolled students have fled the college.
Most schools in the area closed after militants on July 6 killed 29 pupils and a teacher, burning some alive in their hostels, at Mamudo outside Damaturu.
US President Barack Obama on Tuesday described Boko Haram as one of the most vicious terrorist organisations in the world, speaking at a meeting with Jonathan at which both reaffirmed their commitment to fight terrorism.
The Islamic extremists have killed at least 30 other civilians in the past week, including a pastor and his son. And the military said it killed more than 100 militants and lost 16 soldiers in an attack on an extremist stronghold Sept. 21-22.
Human rights groups have accused Nigeria's military of summary killings of civilians in reprisal attacks and no one knows the fate of hundreds of people detained as suspected militants.
Meanwhile, farmers and government officials are fleeing threats of imminent attacks from Boko Haram in the area of the Gwoza Hills, a mountainous region with caves that shelter the militants despite repeated aerial bombardments by the military.
A local government official said there had been a series of attacks in recent weeks. The official, who spoke on condition of anonymity because he feared for his life, said Gwoza town was deserted when he visited it briefly under heavy security escort on Thursday.
He said militants had chased medical officers from the government hospital in Gwoza, which had been treating some victims of attacks, and torched three public schools.
More than 30,000 people have fled to neighbouring Cameroon and Chad and the uprising combined with the military emergency has forced farmers from their fields and vendors from the markets.
The attacks come as Nigeria prepares to celebrate 53 years of independence from Britain on Tuesday and amid political jockeying in the run up to presidential elections next year. Many northern Muslim politicians say they do not want another term for Jonathan, who is from the predominantly Christian south.