Keith Towler said pupil referral units (PRUs) were often seen as an "afterthought" by local authorities, with inconsistent quality across Wales.
He wants the purpose of units to be clarified and to ensure teaching there is as good as mainstream schools.
The Welsh government said action was being taken to share best practice.
The 41 PRUs across Wales teach nearly 600 troubled children, more than two thirds of them boys, primarily with emotional, personal or behavioural problems.
A report by the commissioner outlined several problems which prevented such pupils catching up with their peers:
Mr Towler said lessons could be learned from areas such as Ceredigion, where he was impressed by the "calm and nurturing atmosphere" at the county's PRU, although the picture across Wales was mixed.
"Encouragingly, 53% of learners rated the help they've had at their PRU as excellent but staff at these establishments have told me they feel very isolated from new initiatives and good practice and are seen as a dumping ground for disadvantaged learners," said Mr Towler.
"If we're to see consistent good practice in PRUs, the status needs to be lifted from one which describes it as a 'Cinderella service' to one that recognises its contribution to ensuring that all children and young people achieve their full potential in education."
Mr Towler added that in Pembrokeshire procedures were now in place to improve the treatment of children following  claims that pupils had been locked in a padded "time-out" room at a PRU in Neyland in 2009.
He called on the Welsh government and education officials to issue new guidance on the provision and purpose of PRUs and help their education achieve the same status as that of mainstream schools.
A Welsh government spokesperson said Education Minister Huw Lewis had already discussed the report's main findings with the commissioner.
"We know that good practice exists in PRUs in Wales but the challenge is to mainstream that good practice to help young people back into mainstream education," the spokesperson added.
Special classes for troubled pupils need to improve as many are seen as "dumping grounds" by staff, the children's commissioner has said.