More than 90,000 innocent people have been added to the national DNA database since a landmark human rights ruling that keeping indefinitely the profiles of unconvicted suspects was illegal, according to new figures.

The disclosure comes as the Equality and Human Rights Commission (EHRC) is pressing the Association of Chief Police Officers (ACPO) to withdraw guidance to chief constables to carry on collecting DNA profiles of innocent people. It says it will take enforcement action if the chief constables fail to act.

Liberal Democrat research, based on parliamentary answers, shows that 433, 752 profiles have been added to the DNA database since the ruling by the European court of human rights in Strasbourg on 5 December last year – the equivalent of 1,480 a day.

So far only 611 profiles of people who have been arrested but not convicted of any crime have been removed from the database after individual challenges to chief constables.

The Liberal Democrats say by applying a 2008 Home Office estimate that 20.8% of people on the database are innocent to the current total of 4.8 million it is possible to estimate that the DNA profiles of more than one million innocent people are being retained. This includes an estimated 90,220 added since the ruling.

Jenny Willott, the Liberal Democrat Cabinet Office spokeswoman, said: "It is appalling that the government has allowed over a million people to be added to the DNA database. Despite the European ruling that the practice is a breach of human rights, for every innocent DNA profile removed from the database, around 150 new ones are added."

She said the government's proposals to limit the storage of innocent people's DNA for up to 12 years had been slated by experts, forcing ministers into an embarrassing climbdown in Parliament.

"The Home Office needs to put an end to this scandal by removing all innocent people from the database once and for all," said Willott.

The EHRC has given ACPO 28 days to confirm that the advice to chief constables will be withdrawn and replaced by advice that complies with the law. If ACPO fails to do this, the commission will consider taking formal enforcement action.

John Wadham, the commission's legal director, said: "We can see no reason now why ACPO should not change its guidance on the retention of DNA. The commission recognises that ACPO had been put in a difficult position by the government by this issue, which is why we are offering them the opportunity now to amend their advice and avert future legal action.

"The police are at the forefront of the fight against crime. The importance of this fight cannot be underestimated but it should comply with the government's legal obligation to protect the privacy of innocent people, as outlined by the European court."

The Home Office said earlier this month it was withdrawing a proposal for the retention of DNA profiles from people arrested but not convicted. Ministers said they wanted to keep the profiles of innocent people for between six and 12 years depending on the seriousness of the offence. The measure was dropped from the policing and crime bill when it faced the threat of defeat in the House of Lords. Ministers have said they will bring forward a new proposal after next month's Queen's speech.