As many as 50 students may have been killed in the assault that began at about 1 a.m. Sunday in rural Gujba, Provost Molima Idi Mato of Yobe State College of Agriculture, told The Associated Press.
"They attacked our students while they were sleeping in their hostels, they opened fire at them," he said.
He said he could not give an exact death toll as security forces still are recovering bodies of students mostly aged between 18 and 22.
The Nigerian military has collected 42 bodies and transported 18 wounded students to Damaturu Specialist Hospital, 40 kilometers (25) miles north, said a military intelligence official, who insisted on anonymity because he is not authorized to speak to the press.
The extremists rode into the college in two double-cabin pickup all-terrain vehicles and on motorcycles, some dressed in Nigerian military camouflage 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.
Almost all those killed were Muslims, as is the college's student body, said Adamu Usman, a survivor from Gujba who was helping the wounded at the hospital.
Wailing relatives gathered outside the hospital morgue, where rescue workers laid out bloody bodies in an orderly row on the lawn for family members to identify their 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.
He said there were no security forces stationed at the college despite government assurances that they would be deployed. The state commissioner for education, Mohammmed Lamin, called a news conference two weeks ago urging all schools to reopen and promising protection from soldiers and police.
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.
Northeastern Nigeria is under a military state of emergency to battle an Islamic uprising prosecuted by Boko Haram militants who have killed more than 1,700 people since 2010 in their quest to install an Islamic state, though half the country's 160 million citizens are Christian. Boko Haram means Western education is forbidden in the local Hausa language.
United States President Barack Obama on Tuesday described the group as one of the most vicious terrorist organizations in the world, speaking at a meeting with Nigerian President Goodluck Jonathan at which both reaffirmed their commitment to fight terrorism.
Boko Haram leader Abubakar Shekau last week published a video to prove he is alive and prove false military claims that they might have killed him in an ongoing crackdown.
Government and security officials claim they are winning their war on terror in the northeast but Sunday's attack and others belie those assurances.
The Islamic extremists have killed at least 30 other civilians in the past week.
Twenty-seven people died in separate attacks Wednesday and Thursday night on two villages of Borno state near the northeast border with Cameroon, according to the chairman of the Gamboru-Ngala local government council, Modu-Gana Bukar Sheriiff.
The military spokesman did not respond to requests for information on those attacks, but a security official confirmed the death toll. The official spoke on condition of anonymity because he is not authorized to give information to journalists.
Also Thursday, police said suspected Islamic militants killed a pastor, his son and a village head and torched their Christian church in Dorawa, about 100 kilometers from Damaturu. They said the gunmen used explosives to set fire to the church and five homes.
Meanwhile, farmers and government officials are fleeing threats of imminent attacks from Boko Haram in the area of the Gwoza Hills, a mountainous area 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 and threats of more. 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 he said they had burned down three public schools in the area.
The official said the Gwoza local government has set up offices in Maiduguri, the state capital to the north.
More than 30,000 people have fled the terrorist attacks to neighboring Cameroon and Chad and the uprising combined with the military emergency has forced farmers from their fields and vendors from their markets.
The attacks come as Nigeria prepares to celebrate 52 years of independence from Britain on Tuesday and amid political jockeying in the run up to presidential elections next year with many northern Muslim politicians saying they do not want another term for Jonathan, who is from the predominantly Christian south.