Thousands of patients in the East had to wait more than 20 weeks between a hospital decision to treat them and the start of treatment, a report says.
The SHA has concerns about Bedfordshire and Suffolk
The East of England Strategic Health Authority (SHA) revealed that in September 2006, 6,040 waited more than 20 weeks for an in-patient admission.
This is about 1,200 more than was planned for by the SHA.
The report says there is particular concern about the number of patients waiting in Suffolk and Bedfordshire.
The government is calling for a maximum wait of 20 weeks for 97% of patients.
The report to the SHA's board meeting says the majority of primary care trusts have reduced the number waiting in September compared to August 2006.
Bedfordshire had 482 patients waiting in September compared to 475 in August, but had a target of 298.
Suffolk had 774 patients waiting in September compared to 901 in August, but had a target of 165.
The best performing PCTs were East and North Hertfordshire, Luton, North East Essex, South West Essex, and West Hertfordshire - which all had waiting lists below their targets.
In September it was revealed that the NHS in the eastern region overspent by £230m in the 12 months to April this year.
The SHA singled out a number of Trusts including Norfolk Primary Care Trusts (PCTs) which had a £35m overspend.
Hinchingbrooke Hospital's forecast overspend of £23m was also highlighted.