The three schools, Lundsberg, Grenna, and Sigtuna, are designated as national boarding schools and are financed by a mix of tuition fees and state funding.
But now, following a government review, the schools can only charge boarding fees and no longer any tuition fees.
The move comes after a two-year government review, the results of which were announced on Thursday, and will essentially convert the schools into publicly-funded, privately managed 'free schools'. The schools will be able to receive public money from local authorities, calculated on their pupil numbers in the same way as for other free schools.
Education Minister Jan Björklund said the fact that only children with rich parents were benefiting from the partly publicly-funded schools was simply not good enough.
"If certain schools are allowed to take high student fees then that means it's only the parents with fat wallets who can afford sending their kids there," he told Sveriges Television (SVT).
The director of the Lundsberg school, Johan von Schéele, told SVT that he "welcomed a common framework for all the schools with boarding facilities".
Other changes will see the three schools losing their government grants for foreign students.
The changes are planned to take effect at the beginning of 2016.
All three schools have been subject to public scrutiny of late following reports of violent hazing incident at Lundsberg. A male pupil had his back burned with an iron in one of the boarding houses. The Schools Inspectorate (Skolinspektionen) briefly closed the school, but it was reopened after a court found that the state agency had no right to get involved in what happened outside the class room.
The government review was carried out independent of the incident.