The study said the insult they face at school often force the students from marginalised communities to quit school and start working as labourers, said an AFP report.
The rights groups interviewed more than 160 teachers, principals, parents and students from schools which have large populations of low-caste poor, indigenous tribals and Muslims, to prepare the study report.
Some teachers force kids from lower caste, minority religions to clean toilets
"India's immense project to educate all its children risks falling victim to deeply rooted discrimination by teachers and other school staff against the poor and marginalised," said the report's author Jayshree Bajoria.
"Instead of encouraging children from at-risk communities who are often the first in their families to ever step inside a classroom, teachers often neglect or even mistreat them," she said.
The study finds that students from backward community were called derogatory names, were denied leadership roles and were served food last.
"Some children said they were segregated and neglected because they were considered dirty, while Muslim students said they were called "mullahs", a term for an Islamic cleric, instead of by their names", said the report.
There is no law in the country which punishes those who discriminate in the classroom.