HSJ has learnt that some acute and primary care trusts have calculated the move to international financial reporting standards on 1 April could incur significant extra costs and alter their break-even position.
One of these is Maidstone and Tunbridge Wells trust, whose new 512-bed PFI hospital was given final go-ahead by NHS South East Coast last week.
The£227m deal will cost the trust£35.6m in payments to the private contractor each year.
But the trust has worked out that it could face an extra£19m in revenue costs from the move to the international standards.
Maidstone and Tunbridge Wells estates director Graham Goddard told HSJ the extra cost would arise if the international rules meant that, in contrast to UK rules, the capital value of the PFI scheme would have to appear on the trust's balance sheet.
As well as making the full liability for the debt clear, the balance sheet move could make the trust liable for 3.5 per cent annual capital charges and depreciation costs on its value.
Mr Goddard said the Treasury had set the trust "very clear" affordability parameters for the scheme. These included a cap on level of annual payment to the contractor and the overall capital value.
The scheme was already at the limit of these affordability caps, and the move to international standards could further dent how affordable it was to the trust.
But Mr Goddard said: "The [international standards] extra charges were not one of the parameters set by the Treasury. Until told otherwise, we have to discount [it] as a concern."
A DH spokesperson said it was not able to disclose whether or not it had set aside any additional revenue to help affected trusts pay the extra capital charges they could be liable to pay to the Treasury.
HSJ understands the department may be discussing scrapping the charges altogether.
PricewaterhouseCoopers technical support head Lynn Hine said in the absence of clear DH or Treasury guidance, all NHS finance directors should be modelling the potential impact of a balance sheet move for any existing or future private finance deals.
When an asset such as a PFI building is shown on a balance sheet its value must be spread over its useful life span in the form of a depreciation charge.
Ms Hine said that in effect this meant trusts could become liable for an additional charge on their income account which could affect their ability to break even.