The DCPCR, in a statement, said such a segregation can have an ill-effect on holistic learning and development of students and also negatively impact the social fabric of the country.
The body also asked the school authorities to immediately dissolve the sections and not shuffle it on the basis of religion.
The DCPCR has asked them to tell the reason behind shuffling students on the basis of their religion.
The North Delhi Municipal Corporation (NDMC) on Wednesday evening suspended the in charge of its school after it came to light that there was "segregation" of Hindu and Muslims students into different sections.
The primary school falls in Wazirabad area of north Delhi and administered by the NDMC. The area comes under the Civil Lines Zone of the civic body.
All municipal corporation-run schools in Delhi are till primary level.
(With inputs from agencies.)