Gunfire erupted over the city on Monday and continued into Tuesday, keeping residents afraid to leave their homes.
The clashes follow Sunday's suicide bomb attacks, claimed by Boko Haram militants, on churches in Kaduna state.
They killed 16 people and sparked deadly revenge attacks, killing scores.
An official at Damaturu hospital told the AFP news agency that the gunfire which started on Monday had caused casualties but it was too dangerous for rescue workers to leave the hospital in order to recover any of them.
"We have been holed up in the hospital since yesterday. We can't leave because it is not safe to go out. The morgue is empty now although there are dead bodies on the street," the official is quoted as saying.
In Kaduna city, Reuters reports that Muslim youths have taken to the streets and fired guns, burnt tyres and destroyed a church.
Revenge attacks between Christians and Muslims have been occurring since Sunday's bombings.
Boko Haram has carried out a series of deadly attacks in the past two years.
It wants Islamic law, or Sharia, to be imposed across Nigeria.