According to the study, the state spends Rs 13,512 per student, which is less than the Rs 32,263 spent per student at a Kendriya Vidyalaya.
The spending figures is less than states including Odisha and Chhattisgarh, that are struggling to match the standards in education.
"33 per cent school going children in Rajasthan are socially and economically backward. Also, there is a significant decline in enrollment of girls in upper middle schools," Soha Moitra, regional director of North-CRY said.
Nearly 21.1 per cent school going children are enrolled in primary schools. However, the state spends only 0.03 per cent of Sarv Shiksha Abhiyan budget to bring children to the mainstream and there is no provision to bring children of 14 to 18 years of age group to the mainstream, she added.
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As per the report, enrollment percentage of girls in 2015-16 in primary, middle and upper middle school stood at 83 per cent, 37 per cent and 25 per cent respectively.
The report has suggested to appoint teachers in schools, their training and to focus on children of weaker sections of the society.