The European Court of Human Rights said the database in England and Wales was illegal because it allowed police to indefinitely retain the profiles of people who had been arrested - but never actually charged or found guilty of a crime.
Dominic Casciani, BBC News
Judges at the European Court of Human Rights last year criticised the England and Wales DNA database saying it was completely out of proportion to its aim. Ministers say their proposals answer the court's concerns - but the argument still comes down to whether the police can reasonably retain DNA taken from people who haven't committed a crime.
Ministers defend this as a proportionate tactic that protects the public, rather than a principled but simplistic stand for privacy. The problem is that there is a lack of data on how many crimes have been cracked thanks to retaining DNA from innocent people.
That leaves critics saying anyone in this category has been judged "not guilty - yet". If the plan gets through before the general election, it will be challenged, testing ministers' claims to have balanced privacy with a duty to protect the public.
However, it said the Scottish part of the database was legal because police deleted most of the profiles falling into this category.
The new rules will also apply to Northern Ireland's DNA store, which is run the same way as in England and Wales, the Home Office confirmed.
Unveiling a package of measures to address the court's judgement, the Home Office said the government had come up with a solution that balanced the public's concerns with the legitimate operational needs of the police.
The measures, including new guidance for police forces, will need to go before Parliament. The Conservatives and Liberal Democrats will oppose the plan, saying the system should be the same as in Scotland.
But Home Secretary Alan Johnson said: "It is crucial that we do everything we can to protect the public by preventing crime and bringing offenders to justice.
"The DNA database plays a vital role in helping us do that, providing thousands of crime scene matches every year and helping to put many criminals behind bars where they belong.
"I believe the proposals represent the most proportionate approach to DNA retention, as well as the most effective way of ensuring the database continues to help us tackle crime."
PROPOSED DNA RETENTION RULES
Convicted adults - indefinite
Unconvicted adults - six years
Unconvicted, but arrested for terrorism - possibly indefinite
First minor offence - five years
Second minor or first serious offence - indefinite
Unconvicted 16 to 17-year-olds - six years for serious offence, three years for minor offence
Leander Clifton told BBC News he had ended up on the DNA database after a minor scuffle between his dog and another in the market at Kingston-upon-Thames in Surrey last year.
He was arrested after a woman fell and grazed her hand. At the police station he was stripped and had a DNA sample taken but was released without charge.
Mr Clifton said it had taken more than four months of pressure to have his DNA profile destroyed.
He said: "It's appalling that my civil liberties have been manipulated in this way by a government that is set upon, day by day, tweaking and taking away tiny bits of our civil liberties and thinking no-one will notice. I feel absolutely outraged.
"The government should have the courage to widen the database to every single person in the UK. Either everybody should be on it or no-one - unless they have been convicted of a crime.
"If every person in the UK is on the database then there is equality. As it is there's hardened criminals and perfectly innocent people on it."
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.