Alec Jefferys told journalists on Wednesday the power of the technology was worrying - even though his discovery has revolutionised everything from criminal investigations to family law.
Speaking at a press briefing to mark the 20th anniversary of the discovery, the genetics professor said there were now major issues that needed to be discussed.
In Britain, a national criminal database established in 1995 now contains 2.5 million DNA samples. Countries including the United States and Canada are developing similar systems.
Jeffreys said he feared the stored DNA samples could be used to extract information about a person's medical history, ethnic origin or psychological profile.
And he opposes the practice, approved by a British court in 2002, of retaining DNA samples from suspects who are acquitted and from people arrested but not charged, leading to a "criminal" database that contains many people convicted of no crime.
"My view is, that is discriminatory," Jeffreys said. "It works on a premise that the suspect population, even if innocent, is more likely to offend in the future."
The Home Office, which is in charge of law enforcement, disagreed. "Law-abiding citzens have nothing to fear," said a Home Office spokesman, speaking on condition of anonymity.
Jeffreys advocates a truly national database including every individual, with strict restrictions on what information could be stored.
"In terms of DNA touching people's lives, DNA fingerprinting is probably the most important thing to come out of the discovery of the double helix"
Alec Jeffreys, DNA fingerprinting pioneer
"There is the long-term risk that people can get into these samples and start teasing out additional information" about a person's paternity or risk of disease, he said. "The police have absolutely no right to that sort of information."
The Home Office said it was not considering any plan to establish a database including every citizen.
DNA testing is not an infallible proof of identity. While Jeffreys' original technique compared scores of markers to create an individual "fingerprint", modern commercial DNA profiling compares a number of genetic markers - often 5 or 10 - to calculate a likelihood that the sample belongs to a given individual
Jeffreys estimates the probability of two individuals' DNA profiles matching in the most commonly used tests at between one in a billion and one in a trillion, "which sounds very good indeed until you start thinking about large DNA databases".
In a database of 2.5 million people, a one-in-a-billion probability becomes a one-in-400 chance of at least one match.
Despite his misgivings, Jeffreys believes the technology has done far more good than harm. "I'm absolutely overawed at how this technology has spread. We saw it as a pipe dream in 1984.
"In terms of DNA touching people's lives, DNA fingerprinting is probably the most important thing to come out of the discovery of the double helix."