The bank has invoked the Data Protection Act, which says files should not be kept longer than necessary.
It emerged less than a week after the bank was fined £8.9 million for unfair treatment of 22,000 mortgage customers since 2010.
It is also refusing to review its "embedded swap" loans to thousands of small businesses despite growing political pressure.
Beat The Banks, a PPI claims management specialist, believes the bank has not destroyed or deleted all pre-2006 records, as at times it has been able to produce records dating to 1996.
It has complained to the Information Commissioner's Office, claiming it is the only major bank not to disclose customer information going back at least 15 years.
Clydesdale admitted it was "reviewing" its PPI complaints handling, including the data issue.
Beat The Banks has submitted more than 100 PPI claims to the bank.
In most cases, the Clydesdale responded it is "only required to hold relevant documentation for up to a period of six years", though sometimes it has said seven years and that it holds no information on any of the customer's activity prior to that, potentially killing off the claim.
The organisation estimates its clients might have been paid out £200,000 if claims had been processed.
In addition, internal reference numbers on the bank's correspondence suggest Clydesdale may have had almost 8000 'subject access requests' in 2012, implying a potential pay-out of more than £15m last year alone.
Founder Mike Begg, a former Clydesdale banker, said he could get records for other banks dating to 1995 or 1998 and they must provide disclosure if they have details.
"We can get records going back to 1995 with RBS, Lloyds and Nationwide and 1998 with HBOS. If the bank has the information, it has to give it to you, it can't withhold it.
"The only bank I have a problem with is the Clydesdale, it just will not give out information, I have dozens of empty files, they are normally inches thick."
In August, the bank produced comprehensive account information going back to 2001 for a Dundee woman.
Earlier this year, it disclosed a list of another customer's accounts going back to 1996. When a Broughty Ferry customer objected to the bank's original response and threatened to complain to the Information Commissioner's Office, he promptly received copies of his credit card application from 1999 and subsequent account statements.
Another customer has obtained a copy of a credit card application form from 1997, although Beat The Banks had been told the same customer's pre-2006 records did not exist.
Mr Begg said: "It is impossible for the bank to destroy everything after six years. At times it has produced old files.
"The bank should hold information as long as everybody else does, it just does not want to give it out."
The Financial Conduct Authority said: "Whilst we acknowledge firms have their own data retention policies, this should have no impact on how they address a customer's complaint that stretches back beyond that point."
The Information Commissioner's Office has said it is "not able to make generalisations with regard to a company's compliance" but looks at alleged breaches of the (Data Protection) Act on a case by case basis.
A spokesman for Clydesdale: "We have a clear policy of retaining customer documentation for a minimum of seven years from the date an account is closed or from when a customer ceases to use a service.
"We are in the process of reviewing our PPI complaint handling policy, including this matter.
"We fully recognise our obligation to provide a fair and comprehensive PPI complaint handling process that is not constrained by time period.
"We are committed to delivering the best outcome for customers."
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