ContactPoint, a £224 million database of under-18s, will be fully switched off on 6 August following a phased closure.
Tim Loughton, children’s minister, said the decision had been taken because it was “unjustifiable” to hold the children’s records.
ContactPoint, built by Capgemini, was originally intended to help improve the management of social care for vulnerable children.
But it had become the subject of criticism after concerns emerged over the children’s rights and over any potential security risk over such sensitive data – as hundreds of thousands of people would have had access to the system.
"It has always been our view that it was disproportionate and unjustifiable to hold records on every child in the country, making them accessible to large numbers of people," said Loughton in a written statement to parliament.
The government is considering a “national signposting service” instead, which would aim to help practitioners find out “whether another practitioner is working, or has previously worked, in another authority area with the same vulnerable child".
Loughton has also sent a letter to local managers of children’s services to give them a timetable of the shutdown as well as provide guidance. The database will be destroyed “using government-approved security standards and processes”, according to the Department for Education.