The Age reports that the boy was allegedly asked to leave a Catholic school at Laverton in the city's west.
Altona mother Vida Benic says the school failed to protect her son from discrimination and bullying.
She lodged a complaint with the Human Rights and Equal Opportunity Commission last week. It focuses on the treatment of her 12 year old son Stefan who has a severe language disorder.
The claim names both the Catholic Education Office and Fr Ian Ranson from St Martin de Porres Primary School in Laverton.
In May, the school enrolled the siblings at another primary school without the parents' consent. Anti-discrimination consultant Julie Phillips said she was concerned Stefan's language disorder was the reason the children had effectively been told to leave.
Media reports subsequently caused the school to back down.
Catholic Education Office assistant director David Huggins said the office had been working with the family for a number of months to try to resolve the issues. He said he was surprised and disappointed that the case had been taken to the courts.
Angry mother sues after children told to leave (The Age, 17/9/07)
LINKS (not necessarily endorsed by Church Resources)
St Martin de Porres School, Laverton
Laverton school will not remove students (CathNews, 21/5/07)
Parish priest sends students to another school (CathNews, 18/6/07)