The consumer help website believes tens of thousands of employees who completed widening access training (WAT) schemes could be in line for tax rebates by applying through their NHS trust, after being taxed as if they had undertaken paid work.
Nurses, midwives, health visitors, doctors and psychologists are among those who took part in WAT schemes, undertaking full-time training at colleges and universities. They are designed to broaden the professional knowledge of NHS workers.
MoneySavingExpert.com said it published guidance for NHS practitioners in July on how to claim if they might be eligible.
Since then, it said dozens of NHS staff have tried to reclaim. WAT trainees that MoneySavingExpert.com has spoken to who successfully reclaimed typically get over £1,000 back and one received £13,500.
But others have written to MoneySavingExpert to criticise a lack of clarity on who should be responsible for handling the refunds.
One group of health visitors described it as a "long, laborious, inconsistent process, with several anomalies, limited communication and no explanation for vast differences in amounts paid back".
MoneySavingExpert.com managing editor Guy Anker described the situation as an "utter shambles".
He said: "There is confusion about the rules, variances in what claimants get, and despite it being money they never should have paid in the first place, employees are essentially being put off from getting their money back.
"HMRC (HM Revenue and Customs) needs to issue clear guidance on both tax and national insurance rebates to all trusts and regardless of who's at fault, anyone enrolled in this scheme going forward needs to have the correct deductions made automatically through payroll."
HMRC said the refunds, which only apply to a small fraction of NHS staff who have undertaken training, are being processed quickly in cases where it is provided with all the relevant information.
It has agreed to review cases up to and including 2013 to reduce the administrative burden on the NHS trusts, but said it has always been the responsibility of employers to follow the relevant guidance.
A spokesman for HMRC said: "We are working closely with NHS trusts to ensure that all those who overpaid receive refunds as soon as possible. This may take some time depending on the quality of information provided to us. We ask customers to do some basic checks first before contacting us."
MoneySavingExpert.com has a reclaim guide for those affected at www.moneysavingexpert.com/reclaim/nhs-reclaim.