The children - all aged 15 or under - were taken to a juvenile detention centre in Bauchi on 10 January after spending 12 days in police custody, Adamu Abubakar, head of Nigeria Red Cross (NRC) in Bauchi, told IRIN.
"The 11 children are being held despite our protest. We offered to trace their parents and reunite them but our suggestion was rebuffed by the police authorities," Abubakar told IRIN.
"Our concern is that these 11 children are being held as suspects, which means they would be charged to court," he continued.
Judicial workers are currently on strike in Bauchi, so courts remain closed, which Abubakar fears could extend the children's detention.
According to Abubakar, on 8 January police handed over a further 12 children to the NRC, which went on to reunite them with their parents.
Atiku Kafur, Bauchi State police commissioner, told IRIN: "As far as we are concerned, they [the children] are suspects and will be arraigned before the court of law when the judicial strike ends. The fact that they are minors doesn't mean they should not face justice. If a child commits murder, he should be prosecuted although his punishment will be different from that of an adult."
On 29 December deadly clashes erupted between two factions of the Kala-Kato Islamic sect after its spiritual leader called for the death of those in a breakaway group.
Children killed, displaced
Bauchi Specialist hospital morgue attendants told IRIN on 31 December that they received 67 corpses from the violence, including 22 children and three women. Local police put the death toll from the violence at 38, while the NRC says 40 have died.
The large number of women and children affected in the violence prompted Kaduna-based rights group Civil Rights Congress to call for a probe into alleged extra-judicial killings by Nigerian security agents.
Rights groups have long condemned what they call excessive violence by security forces in cracking down on sectarian clashes, which are common throughout the country. LINKS
"Our men had to use some measure of force to fend off resistance from sect members, killing some of them including their leader," Bauchi State police commissioner Atiku Kafur told reporters.
NRC estimates 65 people whose houses have been destroyed are currently sheltering in the home of the chief of Bauchi's Gwallaga District, 48 of them children who lost a parent in the violence.