Transport arrangements for Catholic children have had to be changed to ensure their safe arrival at school.
Pupils from the Catholic Drumcree high school, who change buses in Portadown town centre, say they have been physically and verbally harassed by pupils of other schools. They tell of being chased through the town and spat on as well as being subjected to sectarian abuse.
A 14-year-old Catholic boy said: "Every time we walked through the town centre they were shouting at us. One group was late for school one day as they had to run off from another crowd before the bus came."
A Catholic boy was taken to hospital after being hit on the head with a stone. A girl seen being buffeted with school bags was later found "very distressed" in a store by the Drumcree high school principal, Seamus O'Neill.
Pupils from both communities blame a small minority for stirring up trouble.
One said: "It started with some name-calling in the town centre as students waited for buses to pick them up. Then a few started getting chased and pushed about."
The children being abused are easily identifiable as Catholics because of their school uniforms.
The local education board last week arranged for a bus to bring 15 children from Armagh straight to school, instead of dropping them off in the town centre.
The remaining pupils at risk have been travelling with Mr O'Neill and other staff. Mr O'Neill said the recent harassment was not an isolated incident. Last year some pupils had to be transported to school in a minibus which is no longer available to Drumcree high.
He said: "I regret segregating the pupils. But I have to. I am in the place of parents when the children are in the school and I must act like a good parent. A good parent must look after the security of the children. We have no choice. Otherwise, someone's going to end up seriously injured or killed, like last year."
Last October Drumcree pupil Darren Murray died after being hit by a van as he ran across the road towards Loyalists who were jeering at him.