The inventor of genetic fingerprinting, Professor Sir Alec Jeffreys, today warns that the government is putting at risk public support for the DNA national database by holding the genetic details of hundreds of thousands of innocent people.

Jeffreys, whose pioneering discoveries revolutionised police investigation techniques, condemned the government for leaving innocent people "branded as criminals" by its insistence on keeping the details of everyone arrested, regardless of whether they are later convicted.

He said he was left "almost speechless" by reports that the government planned to respond to a recent European court ruling - that storing innocent people's genetic details broke their right to privacy - by simply removing their profiles from the database but keeping the original DNA samples.

In an interview with the Guardian, he said: "I have significant concerns there [about the size of the database]. That database is currently populated by an unknown number of entirely innocent people. It is not possible to get an accurate number but it appears to be hundreds of thousands.

"My view is very clear that if you have been convicted of a crime then you owe it to society to be retained on that database for catching in the future should you reoffend. But the retention of entirely innocent people is a whole different issue. There is a sort of presumption here that if they haven't committed any crime now, then they will in the future."

He also called for improved genetic testing procedures, warning that the current system could result in a miscarriage of justice.

Jeffreys' genetic discoveries at Leicester University in the mid-1980s enabled the establishment of the national DNA database 10 years later; it is now the largest in the world, storing details on more than 5 million people.

He believed DNA fingerprinting was a valuable technology and investigative tool which had enjoyed considerable public backing; his concern was the loss of that support.

"My genome is my property. It is not the state's. I will allow the state access to that genome under very strict circumstances. It is an issue of my personal genetic privacy," he said. "I have met some [innocent] people who are on the database and are really distressed by the fact. They feel branded as criminals and I would feel branded as a criminal."

Last December the European court of human rights (ECHR) ruled that the government was violating the rights to privacy of two men from Sheffield whose profiles were being held on the DNA database years after criminal proceedings against them had been dropped.

Asked about reports that the government wanted to get round the implications of the ruling for other innocent people whose details are retained on the database by keeping their original DNA samples, Jeffreys said he was "almost speechless".

"I would be wholly opposed to retaining the original DNA unless there are very, very strict safeguards on what could be done with it, like nothing at all. In a way, it would be even more sinister than retaining the profile.

"I would be very concerned if the government attempted to go down that route. The point is it has to to respond to the ruling by the ECHR. It was a very pointed ruling. Unusually so."

Police in England, Wales and Northern Ireland routinely take DNA samples from everyone arrested on suspicion of committing a recordable offence, which are then added to the national database. In Scotland, DNA records are destroyed if someone is acquitted, apart from in a small number of serious cases.

Jeffreys dismissed the Home Office argument that keeping the genetic details of everyone, even those acquitted, helped solve other crimes. "If you just dumped a few hundred thousand people at random on to the database you'd get the same effect," he said.

"I have never seen any argument in favour of England, Wales and Northern Ireland being the only countries in the world to retain the DNA of entirely innocent people. There are serious issues of discrimination and stigmatisation of branches of society that are over-represented on the database."

He also expressed concern that the current system of trawling the database in search of DNA matches left open the possibility of miscarriages of justice.

"Let's suggest you have two samples that get swapped, and I stress that the likelihood is very low, but given the huge amount of case work one has to be mindful of the fact that there is not a zero probability, then you may get an error. You may have wrong profile and come up with wrong suspect.

"The key point in my view is that cold hits on the database really should be verified by a second round of testing. That would trap false matches which are exceedingly rare but could happen and have happened in one or two cases in the past. I would like to see that in place. And it is not done. It leaves open the possibility of an unsafe conviction."

Following the release from prison last month of Sean Hodgson, who served 27 years after being falsely convicted of murder, Jeffreys called for DNA techniques to be used in more cold case reviews.

"At the moment the way it works is that police look for [cold] cases where they can catch the culprit. What you don't see is the flip side. People who maintain their innocence for decades. Yes, there should be some sort of government funding.

"Spending 27 years in prison for a crime you didn't commit is a terrible thing by any measure of judgment. And DNA could cut through that and it could be used. The state simply has to take it on that the judicial system is not perfect.

"With modest expenditure, you could cut through some of these cases. The key thing is never mind who pays for it, it should be done."