"Our examination system should be trustworthy, should be transparent and the system should make maximum use of technology," Modi said on Instagram, adding that new legislation to deal with paper leaks would be introduced in parliament on Monday.
The measures would tighten the law and toughen the penalties for culprits, Modi added.
It was Modi's first public comment since Education Minister Dharmendra Pradhan resigned on Saturday following the protests by youth activists, who demonstrated for weeks demanding he quit over exam paper leaks in May.
Modi did not mention Pradhan in his 30-second video statement.
The youth-led Cockroach Janta Party (CJP) movement, which spearheaded the demonstrations, called off its protests on Saturday after its demands were met.
The government also accepted the protesters' demands for reforms in the exam system, dropping police cases filed against protesters and compensating families of students who died by suicide after the exam paper leaks.
The CJP, a youth-led movement born out of anger over repeated examination paper leaks, has evolved into India's biggest student mobilisation in years.
Nilekani is an entrepreneur best known for leading the creation of India's digital identity system Aadhaar and co-founding software major Infosys.
