Health secretary Andrew Lansley has written to the NMC calling for an independent assessment of the regulator's proposals to increase registration fees by 58 per cent.
The fee rise would see nurses charged £120 a year compared to £76 currently, with the increased revenue used to help tackle a backlog of fitness to practice hearings.
Nurses and midwives have reacted furiously to the planned increase, with unions deeming it unacceptable at a time when wages are frozen and pension contributions are set to rise.
A spokesman for the DH said it was 'only right' that the NMC explored all possible options to avoid an increase. 'They should be able to justify to their registrants the need for a rise, which is why we have asked them to carry out an independent assessment of their proposals,' he added.
A spokeswoman for the NMC acknowledged receipt of the secretary of state's letter, and said a response would be issued 'in due course'.
The NMC was heavily criticised in a strategic review by the Council for Healthcare Regulatory Excellence last month. It found 'failings at every level' of the regulator, and said it 'lacked proactivity in pursuing cost savings', and had struggled to manage its finances.
Several unions, the RCN, Royal College of Midwives and Unison, have joined forces to urge 'swift and comprehensive' improvements at the NMC, and have welcomed the DH's calls for an independent assessment of the fee increase.
In a joint statement, the unions said: 'We hope to see the terms of reference for the audit as soon as possible, and that those terms will be wide-ranging enough to deliver the change which is needed if the NMC is to be financially sustainable.'
The statement also called for the deadline for submissions to the NMC's consultation on the increase to be extended so that the results of this audit can be taken into account.
'The proposed audit needs to be carried out swiftly and its recommendations taken on board. This is essential for nurses and midwives to have confidence in the NMC as their regulator,' it added.