Some NHS staff in England say they are not receiving an extra one-off payment awarded by the government as part of the latest pay deal for nurses and other workers such as ambulance crews.
The issue is affecting some "bank" staff, who provide temporary cover for hospital trusts to fill rota gaps.
Some say they have not received the lump sum, of at least Â£1,655.
It was part of the new pay agreement for more than a million NHS workers, in addition to a 5% rise.
The Unite union has accused ministers of a cynical ploy.
The Department of Health and Social Care says the deal, agreed with most unions, involved a one-off payment for staff directly employed by NHS organisations - but for those on locally managed contracts, such as bank staff, it was up to individual employers to determine pay and conditions.
One staff nurse, from Liverpool, has started a petition asking the government to ensure all NHS bank staff in England receive the non-consolidated payments.
Bank staff are not employed on the national Agenda for Change contract other nurses and healthcare staff fall under.
The bank allows NHS staff at a trust to work extra shifts - but some health workers work only for the bank, taking whatever shifts are offered, and some of these have found they did not qualify for the one-off payment, even though all their work is for the NHS.
Some bank workers are paid the same rates as staff at the same employer, with some holiday and sick pay.
But others, in exchange for flexibility over hours, can be paid more per hour though without the same employment protection.
Arrangements vary trust by trust.
'Extend funding'
Yorkshire Ambulance Service has decided to pay the lump sum to some workers, including those who work for the bank.
An official said: "Yorkshire Ambulance Service NHS Trust reviewed the contracts of its bank-only staff and determined that they should receive the one-off payment as per contractual obligations."
Northumbria Healthcare which runs hospitals in the North East has done the same.
But the trusts that have chosen to have to do this from their own resources.
Other employers have chosen not to and are being pressed by health unions to change their policies.
Unite says the government should extend funding made available for trusts to make the payments to staff, to allow them to include bank workers.
'Two-tier system'
General secretary Sharon Graham said: "The cynical ploy of saying that NHS bank staff - or any other NHS staff - should get a pay increase on the one hand, but then refuse to fund it on the other, is yet another case of ministers robbing Peter to pay Paul.
"Telling local trusts that they must find cash out of existing funds means one thing and one thing only - more cuts to a health service already on its knees.
"More cuts means more overworked and demoralised staff walking away and on it goes."
Health staff at other organisations, deemed "non-statutory", for example in nursing homes and GP services, have also missed out on the payments.
The NHS Confederation has called on ministers to intervene, warning there is a danger of a two-tier system being created.
The Agenda for Change pay deal covers most NHS staff, except doctors and dentists, who are on a different contract.
It was reached after a series of strikes by workers over concerns about rising inflation outstripping pay awards.