The incident happened in Jomba, a town in the eastern province of Nord-Kivu -- which has been the focus of new clashes between Nkunda's men and the army of President Joseph Kabila.
"These children ran from their primary schools, from their secondary schools in Jomba. They walked all the way to Rutshuru, 15 kilometres (10 miles) to the north west and they are now in the stadium at Rutshuru," Paul Ndeze, tribal chief in the region, told AFP.
Ndeze called for emergency aid to be dispatched for the children calling the situation "horrendous". He said the youngest were eight and the oldest 17-18.
The children -- mostly ethnic Hutus -- fled the clutches of Tutsi leader Nkunda's National Congress for the Defence of the People (CNDP), according to local residents who took supplies to the children.
Nkunda and government forces were in a tense standoff after the expiry of a deadline for rebel forces to lay down their weapons and be integrated into the army.
Kinshasa, which has deployed 15,000 troops in Nord-Kivu, had given rebels backing Nkunda until Monday night to demobilize before launching an offensive.
But on Monday night defence minister Diemu Chikez warned rebels that they would be classified as "criminals" once the deadline for disarming ran out.
The two sides have exchanged gunfire in recent days whilst the head of the UN's peacekeeping mission has urged Nkunda's forces to lay down their arms.