The home secretary, Jacqui Smith, will publish plans this week for the destruction of the DNA profiles of nearly a million innocent people from the police national database. The government's response follows a ruling by the European court of human rights last year that the practice of retaining the DNA profiles was illegal.

In a retreat from plans to get round the judgment, first reported in the Guardian in February, the new proposals will also include the destruction of all physical samples, such as mouth swabs, hair and blood. They will be published in a consultation paper on forensics.

Smith told the Observer today that there were genuine concerns over the size and scope of the DNA database. "It is crucial that we do everything we can to keep the public safe from crime and bring offenders to justice," she said.

"The DNA database plays a vital role in helping us do that. However, there has to be a balance between the need to protect the public and respecting their rights. Based on risks versus benefits, our view is that we can now destroy all samples."

Of the 5.1 million people on the database, about 800,000 have no criminal conviction; they may have been arrested and never charged, or taken to court and found not guilty. After the court ruling last December which criticised the "blanket and indiscriminate nature" of the UK regime, Smith ordered the profiles of all young children to be removed immediately, and indicated that time limits would be introduced for those not convicted of any crime.

Civil liberty groups will be anxious to see how long the police are allowed to keep the DNA data before they are required to remove it. While Home Office officials say the decision to destroy samples as well goes further than the European court ruling, critics say that the measures do not go far enough.

"The DNA database is already too big," said Simon Davies, director of the campaign group Privacy International. "We would argue that the samples of anyone convicted of even minor offences should be removed."

The Conservatives, who have argued that allowing the government to store the DNA data of anyone questioned by the police "represents an unacceptable extension of the power of the state", are unlikely to be content with the government's retreat. They would like to see England and Wales adopt a similar system to Scotland, which allows the DNA of adults charged with sexual or violent offences to be stored for three years. The shadow home secretary, Chris Grayling, writing on theguardian.com after the European court ruling, said: "There is nothing to consult about. The situation is straightforward. It's illegal. So stop."

Although no one concerned with the criminal justice system denies the importance of DNA forensic evidence, there are fears that officials will now attempt to collect stronger evidence of how the use of DNA evidence solves crimes, after the court said it would need "weighty reasons" to justify the current scale of the police database.

The Home Office says that between April 1998 and September 2008, there were more than 390,000 crimes with DNA matches.

But its own evidence to the European court showed it did not have figures for any crimes solved by stored DNA data from unconvicted people. A barrister in the case, Stephen Cragg, told the Guardian recently: "The majority of examples provided by the government involved matching suspects' DNA with crime scene stains. These cases did not involve samples retained from innocent people."