There are about 100 potentially unsafe convictions being investigated, according to a group that campaigns for people wrongly put behind bars.
His comments come as Sam Hallam, 24, spends his first weekend of freedom after seven years in prison.
The Court of Appeal ruled this week that his conviction was "unsafe".
Mr Hallam was jailed in 2005 for a minimum of 12 years over the death of Essayas Kassahun, 21, in Clerkenwell, central London, in 2004.
After his release, he said: "I don't want anyone else ever to suffer what I've been through."
Mr Hallam, who lost a conviction appeal in 2007, also thanked the Criminal Cases Review Commission (CCRC) and Thames Valley Police for the "thorough investigation" they carried out into his case.
Speaking on BBC Radio 4's Today programme, Dr Naughton said that it was a "fantastic time" for Sam Hallam and his family. But he warned that it is not an isolated case.
The system isn't about innocence and guilty in the way that ordinary people might think it is”
"I'm not saying that there are thousands and thousands of people in prison who shouldn't be there. There are certainly thousands of people in prison who say they shouldn't be there but that's a different matter.
"We have a hundred cases being worked on in our 26 Innocence projects and universities around the country.
"And those universities are serious universities - not just Bristol University but Cambridge, Exeter, Durham. There's a long list of universities working on these cases."
He criticised the CCRC for "factually guilty" people having their convictions overturned on technicalities.
"The system isn't about innocence and guilty in the way that ordinary people might think it is. And Sam Hallam overturned his case because there's non-disclosure in his case, so there's an abuse of process.
"In the cases we are working on, we have serious doubts about the evidence leading to their convictions, because of the research and the work that we've done."
But many of these cases won't be referred because they don't fulfil CCRC criteria about evidence available at the time of the original trial, he said.
"What we are calling for are reforms of the CCRC so that it can be better placed to assist people who apply to it who might be innocent."
Miscarriage of justice
Richard Foster, chairman of the CCRC, said: "The test that we apply, the test of safety, is a statutory test. It's not one that we made up ourselves.
"Safety is a test for all of us. If you or I is being prosecuted in court, then you want the processes to be fair as well as the outcome being the right one."
People can be guilty but still suffer a miscarriage of justice, Mr Foster said, pointing to the example of a woman who pleaded guilty to stealing a passport, money and trying to escape the country.
What on the outside may look like a clear case of guilt was not, he said, because she was trafficked to the UK, held in a house and forced into prostitution. She escaped and committed the crimes trying to flee the country.
"Justice was only done because we referred that case," he said