The Post Office has been criticised for its handling of the Horizon accounting software issues in a leaked report.
In January last year, it announced it would investigate whether the software used by its 11,500 branches was to blame for unexpected losses.
Around 150 subpostmasters and mistresses claim they have had to wrongly pay for discrepancies, have been fined and in some cases imprisoned, due to the error.
Subpostmasters are, under contract, responsible for deficits by their branches.
Action group Justice for Subpostmasters Alliance (JFSA) claims Horizon software, used by thousands of Post Offices nationwide, is to blame for these accounting discrepancies in some cases.
However the Post Office has denied that there is a problem with the system.
External investigators Second Sight has been examining the allegations since June 2012. It has since published an interim report. However a new, unpublished report has been seen and reported on by BBC News and Private Eye.
According to the BBC, the leaked report criticises the technology, stating it was not fit for purpose in some branches. It reportedly added that investigators did not look for the root cause of the errors but instead accused the subpostmasters of false accounting.
The report added that training given to those without IT skills was "not good enough" and that equipment had been outdated. Power cuts and communications had apparently made matters worse, it said.
The software, implemented in 1995, is used by more than 78,000 people across 11,500 branches and processes six million transactions per day.
According to Private Eye, the investigators seem to have "defaulted to seeking evidence that would support a charge of false accounting, rather than carrying out an investigation into the root cause of any suspected problems... investigators seem to have found that recording admissions of false accounting was the key to achieving relatively rapid and inexpensive asset recovery.”
In addition, Private Eye said the report documented "inadequate record keeping" and poor auditing processes.
AccountingWEB was unable to contact Second Sight regarding the report, and the JFSA declined to comment.
Second Sight is working with the JFSA, which was set up in 2009, to help subpostmasters and mistresses who may be afraid of coming forward with information or problems surrounding the software to speak out.
The Post Office said in a statement, while it would not comment on the contents of confidential documents, that after two years of investigation it remains that there is "absolutely no evidence of any systemic issues".