The new NHS property company is likely to charge clinical commissioning groups for any assets it takes ownership of whose costs are not fully met by rents or service charges.

It has previously been estimated that the cost of plugging this cost gap could be £500m annually, most of it relating to buildings currently owned by primary care trusts on which other providers pay below-market rents.

A letter sent out to PCTs last week by Department of Health commercial director Peter Coates asked them to repeat an audit of property related costs and income as part of the preparations to transfer much of the estate to NHS Property Services Ltd.

The company will take ownership of a £5bn portfolio of 3,600 properties currently owned by PCTs and strategic health authorities.

The audit was first done in the summer, but the letter says that both the “quantum of cost” and how much of those costs are borne by tenants such as GP practices or community providers, will have since changed significantly.

The exercise will identify where outgoings associated with owning the building are not met by rents or other charges. Many primary care or community care assets are understood to be run on an informal basis, and in some cases cost gaps are cross subsidised through general PCT funding. PCTs also own tracts of land or empty buildings with no income attached.

Mr Coates wrote that the new audit “will enable NHS [Property Services] to recover all property related costs from building users and the appropriate commissioner”.

It is the first clear indication that the property company is likely to charge CCGs for properties previously owned by PCTs which had not set up tenancies to bring in enough income to cover property costs.

Two well connected sources told HSJ the cost gap identified in the summer audit could be as much as £500m a year. However, this could since have reduced if PCTs have increased rents.

John Hargreaves, a partner at Penningtons solicitors, said CCGs “could take it on the chin”, or would have to work with the property company to “rationalise the estate and obtain best value out of it”.

David Lawrence, head of health at property consultancy Capital Symonds, said this type of transfer of public sector assets often revealed “a gap between property costs and income generated from rent and service charges”.

However, “more important” was any gap in compliance with statutory standards such as those around health and safety, and the costs of putting it right. “This will need to be addressed as a priority,” he said.