A quarter of all the largest public-sector database projects, including the ID cards register, are fundamentally flawed and clearly breach European data protection and rights laws, according to a report published today.

Claiming to be the most comprehensive map so far of Britain's "database state", the report says that 11 of the 46 biggest schemes, including the national DNA database and the Contactpoint index of all children in England, should be given a "red light" and immediately scrapped or redesigned.

The report, Database State by the Joseph Rowntree Reform Trust, says that more than half of Whitehall's 46 databases and systems have significant problems with privacy or effectiveness, and could fall foul of a legal challenge.

Only six of the 46 systems, including those for fingerprinting, get a "green light" for being effective, proportionate, necessary and established - with a legal basis to guarantee against privacy intrusions. But even some of these databases have operational problems.

A further 29 databases earn an "amber light", meaning they have significant problems including being possibly illegal, and needing to be shrunk or split, or be amended to allow individuals the right to opt out. This group includes the NHS summary care record, the national childhood obesity database, the national pupil database, and the automatic number-plate recognition system.

The study is by members of the Foundation for Information Policy Research, including Ross Anderson, a Cambridge University professor. It says Britain is now the most invasive surveillance state and the worst at protecting privacy of any western democracy.

It highlights the plight of people who have faced database problems, including a single mother anxious that social services would take her child if she talked to a GP about post-natal depression, and a13-year-old girl left with a criminal record for life because of a playground incident.

The authors estimate that £16bn a year is being spent on public sector IT, with a further £105bn of expenditure planned for the next five years.

Whitehall has admitted that only 30% of public-sector IT projects are successful. There are now thousands of databases operating in Whitehall. The Serious Organised Crime Agency inherited 500 when it was created, and is now attempting to rationalise them into 50 or 60.

Anderson, the professor of security engineering at Cambridge, said: "Britain's database state has become a financial, ethical and administrative disaster, which is penalising some of the most vulnerable [in] society. It also wastes billions of pounds a year and often damages service delivery rather than improving it."

Too often computerisation had been a substitute for public service reform, with little thought given to safety, privacy or value for money. "There must be urgent and radical change in the public-sector database culture so that the state remains our servant ,not our master ... we have to develop systems that put people first."

The report says children in particular are placed at risk. Three of the largest databases set up to support the young are failing to achieve their aims, it says.

Terri Dowty, of Action on Rights for Children, said young people had never been so measured, graded, monitored and discussed; the level of intrusion could not be "justified on the basis of good intentions".

The report raises concerns about the Home Office system, ONSET, which gathers information from many sources to predict which children will offend. The report says children could be stigmatised by a system that contravenes the European convention on human rights.

The Rowntree report says databases given an "amber" light should be assessed for their impact on privacy. Sensitive personal information should normally only be collected and shared with the subject's consent; and datasharing occur only in strictly defined circumstances. "The UK needs information systems that support citizens and professionals on a human scale, rather than multi-billion pound centralised databases used to stigmatise and snoop," said the report's co-author, Ian Brown, of the Oxford Internet Institute.

• This article was amended on Monday 30 March 2009. We described the TV Licensing database as a Whitehall system. The TV Licensing database is owned by the BBC and the information on it is used solely for TV licensing purposes. This has been corrected.