The National Pharmacy Association has called on the Scottish Government to compensate pharmacies left in “financial chaos” by a “shambles” of a faulty payment system that was only introduced last year.

The NPA urged Scotland’s health secretary Neil Gray to intervene after receiving reports from its members that the data capture validation and pricing process, introduced by NHS National Services Scotland (NHS NSS) to process payments to pharmacies, dispensing doctors and medical appliance suppliers, had left them underpaid.

Some pharmacies, the NPA revealed, were facing shortfalls of tens of thousands pounds because of the system’s errors while NHS boards clawed money back from pharmacies with little warning after processing errors had initially resulted in an overpayment.

“A full year after the system was launched, pharmacies are still reporting significant problems and still have no notice nor clarity of what they are getting paid,” the NPA said.

Its chief executive, Paul Rees, said the errors had left pharmacies unable to plan their budgets and settle their accounts, including paying medicine suppliers.

“In the 21st century we should not be facing a computer shambles of this nature. It’s just wrong that hard working community pharmacies should be facing financial stress because an IT system cannot get its sums right,” he said.

“We believe ministers bear ultimate responsibility for this, so they should intervene to make sure the system is fit for purpose – providing timely and accurate information and paying pharmacies the money they are owed and also compensating those who have lost out.”

Martin Morrison, associate director at NHS NSS, told Independent Community Pharmacist it continues to “remedy any remaining payment issues promptly” and insisted it was “committed to working closely with community pharmacies, NHS boards, Community Pharmacy Scotland and other stakeholders to ensure accurate payments and clear communications are provided”.

“We acknowledge the challenges faced by pharmacy contractors since July 2023 during the introduction of a new national IT system for over 1,200 community pharmacies in Scotland. We have been transparent about these issues and have worked closely with Community Pharmacy Scotland throughout,” Morrison said.

“The new system, replacing a 20-year-old predecessor, supports electronic claims and future payments. We recognise and apologise for the impact of these issues and thank everyone for their patience as we resolved them.

“In July 2023, we implemented an interim payment solution using estimates based on recent claiming activity, ensuring no community pharmacy was left short due to the use of estimated payments. As of February 2024, payments are now based on actual dispensed items. Overpayments have been addressed, with a reconciliation completed and independently audited.”