Thousands of DNA profiles of suspected sex offenders are being deleted from the national database because of Home Office incompetence, Labour claims.
A ban on police in England and Wales indefinitely holding the DNA of people not charged takes effect in October.
The Home Office has ordered forces to delete such records ahead of the change, even though an appeals system is not in place, Labour says.
However, the government said it is "restoring common sense to the system".
A Home Office spokesperson said: "In the past, DNA was kept from innocent people, but not taken from prisoners. We are taking samples from the guilty and getting rid of them when people have done nothing wrong."
The records include DNA of 18,000 people held but not charged with rape.
Although police will be required to delete most profiles of people who are innocent and released without charge under the new law, chiefs will be able to ask the biometrics commissioner for permission to hold a sample for three years where the individual is suspected of a serious offence, such as rape, and officers have grounds to do so.
The changes to the National DNA Database came in 2012's Protection of Freedoms Bill, following a major defeat for the police at the European Court of Human Rights.
That 2008 judgement said England and Wales should mirror the Scottish system under which DNA profiles taken from people who are never charged with an offence should be destroyed.
Previous to this judgement, Police in England and Wales could previously hold profiles indefinitely.
The process is designed to allow detectives to hold on to the records of individuals they strongly suspect of serious offences which can be difficult to bring to court, such as rape.
But that appeal process is not yet in place - and Labour says forces are following a Home Office order to delete records in preparation for the legal changeover.
Shadow Home Secretary Yvette Cooper said the Home Office was guilty of "shocking incompetence" .
Ms Cooper said: "It is appalling that DNA evidence from thousands of rape suspects is now being destroyed contrary to the promises made by the prime minister and home secretary.
"The prime minister assured Parliament that if someone was arrested but not charged with rape, the police would be able to ask to retain the DNA of the suspect. Yet because of Theresa May's incompetence the police are powerless to retain it."
As of May, 1.1 million DNA profiles had been destroyed under the programme to remove innocent people from the database.
The biometrics commissioner, Alastair MacGregor QC, recently said police could hypothetically ask him for permission to retain 60,000 DNA records a year relating to serious crimes, each of which could involve a legal battle.
It is not clear whether all forces are completely following the order or whether some are trying to hold on to profiles ahead of a later appeal.
A Home Office spokesperson added: "Forces will be able to retain DNA from someone arrested and not charged for up to three years, but only with permission from the Biometrics Commissioner. And all DNA samples taken by police are checked against the national database before deletion."