Improvement is expected after “unacceptable” waiting times this winter, the NHS deputy chief executive has said.

In a letter to NHS chief executives David Flory said the government had reinforced its commitment to waiting times.

He said: “I have personally stressed the need to maintain delivery of RTT [referral to treatment] through the meetings that were held with you to “sign off” plans for 2011/12. There can, be no doubt about the importance of delivering improved performance on waiting times, particularly for admitted patients.”

He said it is “unacceptable for performance to fall below the expected standards as it did in February and March 2011”. He said although performance in April had improved 47 organisations were still failing to treat 90 per cent of patients within 18 weeks of referral.

He said: “Recovery plans for the worst performing organisations were requested during the recent planning round. We will be engaging with each SHA team in monitoring the compliance with agreed actions to get performance back on track.”

With reference to the four-hour A&E waiting target he warned that while new quality indicators are being introduced, “waiting time remains a key measure and too many organisations are failing to meet the required standard”.

He pointed out that 19 trusts were currently underperforming and that better performance was expected “in advance of the pressures we will undoubtedly face over the winter months”.