The NHS Commissioning Board has recalculated clinical commissioning groups’ allowances for running costs, prompting claims some may have to consider sacking staff they have just employed.

The board announced CCGs’ recalculated running cost allowances for 2013-14 on Friday. They replace previous figures published in May, which CCGs have been using to plan their structures and commissioning support arrangements.

The new allowances are still set at £25 per head of each group’s population, a figure decided by the government last year, but they are based on new population estimates.

A commissioning board statement said: “The publication of the Office of National Statistics’ 2013 population estimates, based on the 2011 census, has enabled us to provide a revised, up-to-date set of running costs for CCGs… The figures will continue to be revised each year as the ONS revises its estimates.”

The effect on total CCG running costs is a £10.5m increase to £1.34bn. However 79 CCGs have seen a fall from the May figures (see tables).

Central London CCG has lost the largest proportion of its allocation, which has dropped by 6.4 per cent of the previous allocation to £4.7m. The average fall among the 79 is £92,000, and 1.6 per cent of their budget.

The board said it had previously warned CCGs the allocations would be recalculated.

However, several CCG leaders told HSJ the move had been unexpected and meant they needed to reconsider their structures at a late stage. For several, their structures have already been submitted and reviewed for the CCG authorisation process.

One leader said his CCG had “just filled all our structures”. He said for some CCGs it could mean staff who had recently been appointed following a long period of uncertainty could no longer be employed.

The source said his CCG was looking at reducing contingency funds and its spend on GP input to commissioning. That would mean a reduction in either the amount of time spent by GPs on commissioning or the rate of reimbursement.

He said it would also look at “rebadging” some costs – such as clinical input – so they did not need to count against running costs.

NHS Clinical Commissioners senior member and GP Johnny Marshall, an adviser to the commissioning board, said the instability created by the shift raised the question of whether it was right to have a defined allowance.

He said: “It certainly creates some instability. I’m not sure anyone has got any evidence to say [the allowance] is exactly the right amount.”

He said small CCGs were particularly at risk from future changes because they could quickly lose a large proportion of their running allowance. The risk could even press them into mergers with other CCGs, he said.

A commissioning board spokeswoman said: “CCGs were informed in May the figures were indicative and subject to change. In some areas, projected population has decreased, so it is only right their allowance reflects this.”

She said they should have planned for the risk of a reduction, and that “many CCGs have never planned to spend the whole of their allocation, preferring to safeguard themselves from the outset against potential reductions and direct as much funding as possible directly into patient care”.