Military authorities yesterday admitted holding 1,400 terror suspects for months without prosecution, but said a recommendation has now been made for the trial of 500 detainees.
Also, 167 suspects are recommended to be freed while the cases of 614 others are for review, the Defence Headquarters said in Abuja yesterday.
The recommendations were made by a Joint Investigation Team set up by the DHQ in July, to "screen and categorise" those apprehended in the battle against insurgency in the North East.
This is the first time authorities are giving specific numbers of people detained over links with the Boko Haram uprising, which has caused the death of thousands since 2010.
Human rights groups have raised concerns over detentions without trial and other abuses in the military campaign to contain the insurgency.
But authorities have consistently denied wrong doing.
In May, President Goodluck Jonathan ordered the release of women and children detained on Boko Haram links.
Following this, a number of detainees were freed and handed over to their respective state governments.
The DHQ subsequently set up the Joint Investigation Team, whose recommendations have now been forwarded to the Presidency, said Defence spokesman Brig-Gen. Chris Olukolade in a statement.
He said the joint team "has recommended immediate trial of over 500 persons apprehended in the course of security operations against terrorists in Yobe, Borno and Adamawa states.
"The suspects are among the almost 1,400 detainees screened by the team at the detention facilities in Maiduguri, Yola and Damaturu between July and September."
The three detention centres are in Borno, Adamawa and Yobe states, which have been under a state of emergency since May.
The DHQ statement did not say specifically if there are other Boko Haram detainees in these three states or elsewhere, apart from the stated 1,400.
It was also silent on the remaining 119 suspects who are not among the total 1,281 being recommended for trial, to be freed or to have their cases reviewed.
"Those recommended for immediate trial include high profile suspects some of whom were training other terrorists in weapon handling as well as those who confessed to being trained in Mali and other countries for the purpose of perpetrating terror in Nigeria," Olukolade said in the statement.
"Also among those recommended for trial are a medical doctor, paramilitary or service personnel who were fighting on the side of the terrorists and other individuals who offered direct logistics support to the terrorists.
"The team however recommended the release of 167 of the detainees from detention in Maiduguri, Yola and Damaturu. About 614 others whose cases were inconclusive have been recommended for review.
"The report also proposed that some of the detainees be tried for other offences ranging from armed robbery, murder to drugs related offences."
Olukolade said the 19-member Joint Investigation Team comprised senior officers from the military, police, officials of Federal and state ministries of justice as well as officers of Immigration, Prisons and Customs.
The team was mandated "to screen and categorise detainees apprehended in the course of operations in the North East," so as to decongest detention facilities in the area of operations and to ensure expeditious prosecution of suspects.
Olukolade said the team was "tasked to examine, classify and recommend appropriate actions against detainees in the various detention centres" in the three states.