Clinical commissioners have raised concern about a “top slice” to their budgets to fund a shortfall in the earnings of the new national NHS property company.

NHS Property Services Ltd took ownership of assets previously owned by primary care trusts and strategic health authorities at the beginning of April. Its portfolio includes community health centres, GP surgeries, offices inhabited by NHS commissioners, and empty properties.

There is a shortfall between its income from rent and the cost of owning and maintaining the estate. NHS Property Services had previously announced that new commissioners would have to fund this difference.

The cost has since been identified and the firm’s finance director Caroline Rassell this month wrote to CCGs to tell them what they will be charged.

The total charge to CCGs based on current estimates for 2013-14 is £180m, HSJ has been told. The charge to NHS England is £109m, which will be divided between the organisation’s central and local area team budgets.

One CCG source said the organisation was told last week it would have to pay £777,000. The source said: “This is the first we were aware of the amount, and represents 16 per cent of our running costs.”

Another CCG reported being billed £300,000 in quarter one, even though it received no direct services from NHS Property Services, while other CCGs have been hit with charges of around £3m.

The charges are based on reports sent by primary care trusts to the Department of Health in February. They depend on the nature of properties in each area and rental agreements NHS Property Services has inherited from PCTs.

This means charges to CCGs depend on whether their predecessor PCTs had rental arrangements in place which covered the cost of running property.

Some CCGs are understood to be frustrated that the charges have been agreed by NHS England and NHS Property Services Ltd, and that the charging system is not open to challenge.

NHS Property Services and NHS England are understood to be in talks about funding in 2014-15. It is intended the costs of running the portfolio will eventually be borne by tenants.

The property company has argued it inherited the shortfall from PCTs, which has always been funded by commissioning budgets in the past.

A spokesman said: “We are making the system we have inherited more fair and transparent. Overall there is no change in the amounts involved but inevitably they are shared differently due to the new organisations involved.

“PCTs were asked to identify which commissioner should pick up these costs and we are honouring those arrangements.”

NHS Clinical Commissioners president Charles Alessi said the charges were “yet another top slice” for CCG budgets, and were “not helpful”.

He told HSJ: “The shortfall is something most of us were completely unaware of. The money could well have been committed by now.”

  • UPDATE May 24 6.30pm. The figures for the total charges for 2013-14 have been changed. An earlier version of this story contained figures based on inaccurate information given to HSJ by NHS Property Services Ltd.