Bachpan Bachao Andolan (BBA) said 1,17,480 children went missing in 392 districts between January, 2008, to January, 2010, as per data collected from government agencies.
In its book 'Missing Children of India', the NGO said it collected the data through RTI from 392 districts and said these children are being trafficked and exploited.
"Police and law and enforcement agencies do not take such cases seriously. There is dearth of agencies for collecting and disseminating data on missing children," Sunil Krishna, Director-General, National Human Rights Commission, said after the study was released.
The BBA also launched a website where one can access nationwide record and data about missing children.
In 2004-05, the NHRC reported that an estimated 44,000 children go missing every year with one-fourth of them remaining untraced. The number has shown an increase of 32 per cent over a period of seven years.
In 5 years, the number and the percentage of children who missing and remain untraced shot up by more than 30 per cent, the book said.
"If the average number of 150 reported missing children per district (from available data) is extrapolated to all 640 districts in the country, the total number of missing children in India every year would come to the tune of 96,000," the report said.
According to the data obtained through RTI, 24,744 children have been reported missing from metros like New Delhi, Mumbai, Kolkata, Chennai and Hyderabad. Among the Metros, Delhi tops the list with 12 per cent of total reported missing children still untraced.
Each year 6,785 children disappear from Delhi with 850 remaining untraced. Out of the total untraced children from these metro cities, Delhi and Kolkata alone constitute 89 per cent.
Among 20 states and four Union Territories, Maharashtra has highest number of children reported missing with 26,211, followed by West Bengal (25,413), Delhi (13,570) and Madhya Pradesh (12,777).
The report also highlights the plight of migrant families residing in semi-urban areas, specially those close to the state, district and international borders.
"Urban centres have high number of children reported missing. Areas with better transport and communication connectivity have high number of missing children. Also, regions with migratory population like slums and families from socially and economically poorer backgrounds form the majority of victims," the report said.
The report has also laid down few guidelines and recommendations to create awareness and find solutions to increasing number of such cases.
P M Nair, ADG (Operations), CRPF said: "We are the part of the system and need to take strong action collectively as well as individually to solve the problem.
"It is the pull factor that is more potent in this phenomena than the push factor. The children from poor families are more vulnerable and need to be identified for prevention."
Justice Altamas Kabir, Supreme Court Judge and Executive Chairperson of National Legal Services Authority said defining the term 'Missing Children' is difficult but not impossible.
"We propose a nationwide linkage of legal system to the remotest part of the country in order to tackle the problem," he said and asked BBA to help solving the problem of missing children.