Avicenna members requesting checks on their prescription payments last year were underpaid by a total of almost £310,000 over a two-year period.
An analysis of the 70 members that requested checks on their payments from NHS Prescription Services (NHS PS), found that 65 were underpaid, with an average underpayment of £4,421. The highest underpayment was £25,506 for one business across five branches.
The average underpayment was £4,421 while the highest for one contractor was £25,506 across five branches
The results come after contractors were given the option last December to check their payments for prescriptions dated between April 2009 and March 2011.
Those opting to do so risked losing a £500 pricing error compensatory payment if they were found to have been underpaid by less than £750 over the period.
NHS PS has not yet revealed the full results of the rechecks it had to do, but Avicenna members said they were "absolutely shocked" by the results they had seen, with several saying they were glad they had risked having the checks.
"My staff do check the prescriptions thoroughly and are very good but I am astonished to find that we were still underpaid," said Sunil Patel of Hyperchem Group, who was underpaid by £25,506 across his five branches.
"This needs to be addressed at a national level since I am positive that a lot of contractors who did not ask for a recheck will have lost a lot of money," said Mr Patel.
Fellow Avicenna member Dilip Maroo from Westbourne Pharmacy lost the most money for a single pharmacy, being underpaid by £24,917 at his one branch.
Mr Maroo highlighted the lack of transparency in the checking process, warning that he had not received a breakdown of the shortfalls from NHS PS.
Contractor Yogesh Patel said he was "absolutely shocked" at what was going on, saying: "If this was the other way around, I would be accused of fraud and probably be serving a jail sentence".
Others threatened legal action against NHS PS, with Sushma Shah proposing contractors club together to challenge the pay master: "There are so many contractors fighting individual battles, why will they not stand up together to fight for money that we have rightly earned?" she asked.
"The margin of error is unexpectedly high," said Salim Jetha, CEO of Avicenna.
"Also worrying is the total lack of transparency about where the errors lie and the lack of accountability of NHS PS," he added.
Mr Jetha called for a higher level of retrospective compensatory payment to be made to contractors and said PSNC needed to "challenge whether NHS PS is fit for the future".
Do you think your pharmacy may have been underpaid?