Secondary schools are perceived to be "highly ineffective" in stopping bullying and racial harassment of Gypsy and traveller children, which can be a strong factor in their self-exclusion.
An inquiry by the Scottish Parliament's equal opportunities committee concludes that schools, especially secondaries, are not yet safe places for them to attend.
Gwynedd Lloyd, head of the educational studies department at Edinburgh University, told MSPs on the committee: "One of the stunning things about the evidence on what happens to Gypsy traveller kids in schools is that every single one of them talks about racial harassment."
Dr Lloyd said that a "little chip" had been made in the "centuries of prejudice and discrimination" against the children and their families since MSPs last raised concerns in 2001.
The MSPs' update also notes that many Gypsy and traveller children do not see the secondary curriculum as relevant to their way of life, which is another reason for their non-attendance.
One land-based course in Perth and Kinross, however, had proved particularly popular as it helped those who took it to find work as ghillies, forestry workers and farm workers.
Many Gypsy and traveller children were successful students in secondaries but MSPs heard that "there was a tendency for many children to hide their identity". One witness said that a teacher had advised her daughter "not to let on to the other kids".
Primary schooling is valued by Gypsies and travellers for providing relevant skills.
MSPs are now calling for alternative ways of reaching children, such as on-site classes and distance learning. Practice varies across the country.