The Sudanese Doctors Central Committee claimed snipers shot at the high school pupils while attempting to break up the demonstration in the city of El-Obeid.
At least five died of their injuries, including the four students and an adult, and more than a dozen were wounded, it was claimed.
The killings sparked calls from the Sudanese Professionals’ Association, which has spearheaded recent protests, for a nationwide demonstration to condemn the violence.
Videos posted on social media appeared to show hundreds of pupils, with school bags on their backs, taking part in the demonstration while chanting “blood for blood, we will not accept blood money”.
Activists recounted how trucks with paramilitary rapid support forces moved in to disperse the protesters using live ammunition.
“Most of the wounded have been shot in the legs, heads and stomach,” said Mustafa Mohammed, a doctor at the main hospital in the city.
The military overthrew Mr al-Bashir in a coup in April but street protests have continued with calls for transition to civilian rule.
Tensions have remained high since June when armed men in military fatigues stormed an encampment of activists outside Khartoum’s military headquarters.
Monday’s protest in El-Obeid took place hours before talks begin between the military council and the protest coalition, Forces for Declaration of Freedom and Change.
Sediq Yousef, a negotiator for the protest coalition, said there should be no further talks with the military until it halted its “violations.”
“We cannot sit at a negotiating table with those who allow the killing of revolutionaries,” he said.
Earlier this month both sides reached a power-sharing agreement earlier this month, which would see joint civilian-military rule for three years while elections are organised.
They remain divided on a number of key issues, however, including whether military commanders should be immune from prosecution for violence against protesters.
Additional reporting by agencies
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