"Our research suggests that the overwhelming majority of police forces are unable to separate the records of people never charged from those found guilty in court."
Since 2004, police forces have been allowed to take the DNA or fingerprints of anyone aged over 10 who was arrested for a "recordable offence", which means most crimes.
The national DNA database grew to include details of several million people over the next few years, and was credited with leading to convictions as samples taken from crime scenes were linked to people arrested for unrelated offences.
In 2008 the European Court of Human Rights ruled that keeping the records indefinitely was unlawful, prompting the Labour government to review the policy.
After the election, the Coalition promised to improve the system by making it more like that of Scotland, where only the DNA of those convicted of serious offences, such as violence or sex crimes, is held and for a maximum of five years.
But it then emerged that ministers only planned to anonymise the records rather than deleting them completely, and did not introduce a safeguard that would mean a judge's approval was needed to keep the files.
The Protection of Freedoms Act - passed last month - also allows biometric material from innocent people to be kept for up if it is deemed to be in the interests of "national security".
Big Brother Watch claims it is not clear how citizens can have their profiles removed from the database, and that in the absence of detailed plans or a timetable from the Home Office, police forces are continuing to add to it.
Figures show there are now some 6.4m profiles on the database.
Records obtained through Freedom of Information requests by Big Brother Watch suggest that 986,767 samples of DNA were gathered between January 2009 and December 2011.
Based on previous estimates, about one in six of these (164,461) are thought to have been cleared or never charged with any offence.
But only 15,966 profiles on people not charged with crimes have been deleted, with most forces refusing to state what proportion of those sampled ended up in court.
Just three forces appear to be able to distinguish the records of the innocent and guilty, and it is estimated it could cost up to £8m to go through the whole database.
A Home Office spokesman said: "The Protection of Freedoms Act - passed into law just a few weeks ago - provides for a clear and robust system to safeguard DNA records. The new regime will be subject to enhanced oversight by a new biometrics commissioner and we are moving forward with implementation.
"Our focus is on keeping the DNA profiles of the guilty not the innocent. DNA profiles of people not charged with an offence will no longer be retained. Those charged with a serious sexual or violent offence will be retained for three years and in special cases can be extended by two years with the approval of a magistrates' court."
The ACPO lead for the DNA database, Amanda Cooper, said: "DNA evidence is a robust and vital technique for police in the detection of crimes. It has been used to not only convict thousands of violent and dangerous criminals but also to exonerate many innocent people.
"There are a number of laws governing how the police can take and retain DNA evidence and the recent Protection of the Freedoms Act makes further changes which are being commenced. The service will continue to take samples and retain profiles appropriately, in accordance with the law, so that we can identify criminals and keep the public safe."
