The court also ordered a Central Bureau of Investigation probe into the attack on social activist Swami Agnivesh during his visit to Maoist-hit Chhattisgarh in March.
"We direct the CBI to take over the investigation into the series of violence and attacks unleashed on Swami Agnivesh and his companions," a bench comprising justices B Sudershan Reddy and S S Nijjar said.
Asking the Chhattisgarh government and the Centre to desist from appointing the tribals as SPOs and arming them for countering the Naxals in any manner directly or indirectly, the court said the appointment of tribal youths as SPOs is "unconstitutional".
The bench said the eligibility criteria including the educational qualification and training of the tribals to combat Maoists goes against the provisions of statutes and the Constitution.
It said the creation of Koya Commandos and Salwa Judum was in violation of the Constitution.
The special police officers have been given the name Koya Commandos after that of a tribe in the Dantewada region.
The issue of SPOs had arisen during the hearing of a petition against the existence of the Salwa Judum (vigilante groups) in Naxal-hit regions of the state to fight Maoists.
The petition was filed by sociologist Nandini Sundar, historian Ramachandra Guha, former bureaucrat E A S Sarma and others seeking a direction to the state government to refrain from allegedly supporting the Salwa Judum.
The issue of attack on Swami Agnivesh was brought before the court in April this year.
Earlier, Agnivesh had said that the Salwa Judum was still active and the chief minister was indulging in double-speak as no FIR has been lodged against any of its members as per the recommendation of the NHRC.
Swami Agnivesh had come to the court in March this year when he was attacked by a group of people allegedly consisting of SPOs and Salwa Judum volunteers -- when he was visiting a Naxal region near Dantewada along with Art of Living activists.
During the last hearing on the issue on May 4, the state government had justified the appointment of SPOs saying they have excelled in performing police duties.
It had also asserted that in anti-Maoist operations, the SPOs were of immense help in their role as guides, translators, spotters and on certain occasions they have saved the lives of regular security personnel while preventing more than dozen Maoist attacks on relief camps and helped security forces in anti-Naxal operations.
However, the court was of the view that arming tribals would lead to a "dangerous" situation if they turned against the State.
The court had also questioned the training programme of the SPOs.
"You are playing with the so-called SPOs. What will happen if they turn against the State. God save this country," the bench had said during the last hearing.