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Latest figures show 6,000 patients in the region waiting more than 12 months for treatment and more than 1,100 waiting over two years.
But health chiefs admit the ring-fencing plan could mean even longer waiting times than at present for patients in emergency departments.
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Jacquie Campbell, chief officer for acute services, told the NHS Lothian board that although the number of out-patients being seen in Lothian had recovered to a higher level than before Covid, in-patient and day cases were only at about 64 per cent of pre-Covid levels and there was a growing problem of waits over one year, 18 months and two years.
She said long waits had an adverse impact on patients, but could also reduce the number of qualified consultants.
"We are seeing an impact on our surgical trainees and the number of cases they are undertaking and that could delay them qualifying as consultants and ultimately have an impact on a timeline for new consultant posts."
The maximum desired occupancy level is 85 per cent. But Ms Campbell said: "It's normal for all three sites to be over 100 per cent occupancy and they definitely don't drop below 95 per cent."
She said to try to address the long waits, the plan was to ring-fence 10 beds at the Royal Infirmary to be used for orthopaedic patients and increase theatre sessions, which would begin to cut the number facing very long waits for hip and knee replacement surgery.
At the Western, five beds will be ring-fenced for urology patients with an increase in theatre sessions too.
And at St John's, day surgery theatre sessions will be increased, helping to address long waits in general surgery, plastic surgery on hands, urology, orthopaedics and ear, nose and throat.
There are also plans to increase ophthalmology sessions at the Eye Pavilion to help reduce very long waits in that field.
But Ms Campbell warned the ring-fencing policy would have an impact elsewhere in the system. "This could mean a higher number of patients in our emergency departments/ front doors, with longer waits."
Latest figures showed just 48.5 per cent of patients at Edinburgh Royal Infirmary’s accident and emergency department were treated within the target time of four hours in the week ending June 12. A total of 1,535 waited more than four hours to be seen.
And Ms Campbell told the board that financial and other constraints meant NHS Lothian would not meet an expected new target for cutting long waits quickly.
She said: "The emerging position from the Scottish Government is that no patient should be waiting longer than two years by March 2023. Within the constraints we currently have and the modelling we have completed that's not achievable for us."