Flaws in the system emerged when staff uploading children's details onto the database found that records, which were supposed to be shielded, were not.
A spokesman for the DCSF said the government is working to address the issues. He said there had been a "few reports" of cases where updates from different sources resulted in information on children who should have been shielded becoming available.
He said: "These are being investigated and if we conclude that we need to adjust the thresholds used by ContactPoint to improve matching, we will do so."
He promised that no child's records would be uploaded onto ContactPoint until the issues are resolved.
Local authorities were supposed to have shielding policies for vulnerable children in place by 13 March.
But Beverley Hughes admitted yesterday that a third of councils have missed the deadline.
The government is working with the local authorities that are behind on their shielding work. But it is still unclear when every council will be ready to roll out the database.
Meanwhile the Information Commissioners' Office is to investigate the Joseph Rowntree Trust's Database State report, which claims that ContactPoint is illegal under human rights and data protection law.
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