Gunbattles continued into Friday evening, hours after Russian commandos appeared to have ended a two-day siege at the school in the town of Beslan in the province of North Ossetia.
Officials said they feared as many 150 people - mainly children - had been found dead at the school. At least 300 people have been wounded, including more than 200 children, Russian news agencies said.
At least 10 of the hostage-takers were reportedly killed in the gun battles.
There are reports that some children are still being held hostage.
There were dramatic scenes on Friday morning after scores of hostages unexpectedly fled under fire. Troops stormed the building where masked men and women had seized hundreds of people, Aljazeera's correspondent said.
More hostages then emerged as Russian commandos entered the building. But heavy gunfire and a series of explosions continued for hours around the area, Salam al-Ubaidy reported.
There have been reports of exchanges of fire between a group of hostage-takers who escaped from the school and Russian troops in pursuit on the outskirts of Beslan.
Earlier, soldiers carried some infants out of the school as ambulances sped to the scene and military helicopters circled overhead. Many of the children were covered in blood.
More than 200 pupils have been
taken to nearby hospitals
Interfax news agency quoted a security official as saying that most of the children who had been taken hostage were alive.
"Those children who remained in the school, in general, did not suffer.
"The ones who suffered were the children in the group which ran from the school and on whom the fighters opened fire," the official was quoted as saying.
It was not clear what had triggered the dramatic battle, a few hours after Russia insisted it would not resort to force to free children, parents and teachers being held for a third day without food or water.
Earlier, several blasts shook the area as armed fighters fired grenades sporadically from the school. One travelled 300 metres before hitting the ground with a huge explosion.
One policeman was wounded
after kidnappers fired grenades
A North Ossetian regional official, Lev Dzugayev, told reporters the fighters appeared to be firing because they thought they detected security forces moving outside.
Quoting a police source, Aljazeera's correspondent said that an explosion left one policeman wounded.
Alexander Dzasokhov, president of the province of North Ossetia, said the armed group had demanded independence for Chechnya in talks on Thursday with Ruslan Aushev, a moderate former leader of neighbouring Ingushetia who has taken on a mediating role.
The school siege is the latest in a wave of attacks in Russia in recent weeks, all linked to Chechen separatists. Last week, human bombers were blamed for the near-simultaneous crash of two passenger planes in which 90 people died.
And this week, in central Moscow another bomber blew herself up, killing nine people.
Earlier, Dzasokhov estimated the number of hostages being held in School No 1 in the town of Beslan at over 500 - above an earlier official estimate of around 350.
Women among a group of hostages freed on Thursday told Russian newspapers the total number of hostages might be as high as 1500.