Police forces in much of the UK could be forced to destroy the DNA details of hundreds of thousands of people with no criminal convictions, after a court ruled today that keeping them breaches human rights.

The European court of human rights in Strasbourg said that keeping innocent people's DNA records on a criminal register breached article eight of the Human Rights Convention, covering the right to respect for private and family life.

Keeping DNA material from those who were "entitled to the presumption of innocence" as they had never been convicted of an offence carried "the risk of stigmatisation", the ruling said.

Attacking the "blanket and indiscriminate nature" of the power to retain data, the judges said protections offered by article eight "would be unacceptably weakened if the use of modern scientific techniques in the criminal justice system were allowed at any cost and without carefully balancing the potential benefits of the extensive use of such techniques against important private-life interests".

The decision could oblige the government to order the destruction of DNA data belonging to those without criminal convictions among the approximately 4.5m records on the England, Wales and Northern Ireland database.

Scotland already destroys DNA samples taken during criminal investigations from people, who are eventually not charged or who are later acquitted.

The home secretary, Jacqui Smith, said existing laws would remain in place while ministers considered the judgment.

"DNA and fingerprinting is vital to the fight against crime, providing the police with more than 3,500 matches a month, and I am disappointed by the European court of human rights' decision," she said.

"The government mounted a robust defence before the court and I strongly believe DNA and fingerprints play an invaluable role in fighting crime and bringing people to justice."

The decision follows a lengthy legal challenge by two British men. Michael Marper, 45, was arrested in March 2001 and charged with harassing his partner, but the case was later dropped.

Separately, a 19-year-old named in court only as "S" was arrested and charged with attempted robbery in January 2001, when he was 12, but he was cleared five months later.

The men, both from Sheffield, asked that their fingerprints, DNA samples and profiles be destroyed. South Yorkshire police refused, saying the details would be retained "to aid criminal investigation".

They applied to the European court after their case was turned down by the House of Lords, which ruled that keeping the information did not breach human rights.