The policy think-tank has made these recommendations in its 'Three-Year Action Agenda, 2017-18 to 2019-20', released recently.
On the modernisation of madrasas, the Aayog has recommended the government make "continued efforts" through curricular reforms and by providing facilities such as computers, labs, libraries, among others.
Madrasa is an Arabic word for an institute that provides education, either religious or mainstream.
Muslims constitute the largest religious minority in the country and according to the agenda they are behind others in terms of economic, health and education parameters.
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"A fee-waiver could also be considered for madrasa students opting for examinations conducted by the National Institute of Open Schooling," the Aayog said in the agenda.
The government think-tank said there were a "large number of madrasas" in the country although the exact numbers are unclear.
The NIOS, formerly known as National Open School (NOS), was established in 1989 as an autonomous body in pursuance of National Policy on Education 1986.
It aims to provide relevant education up to pre-degree level through open and distance-learning system and cater to educational needs of the prioritised target groups.
It has also planned to build toilets in one lakh in madrasas to strengthen Swachh Bharat Mission.
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