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Humza Yousaf said he had met with leaders at the health board and the city council on a weekly basis to discuss the bed blocking issues.
In October, there were 8,169 bed days occupied by delayed discharges in NHS Lothian.
At the Scottish Parliament on Tuesday, MSP Daniel Johnson said he and others had taken part in a briefing on Friday which “painted an alarming picture” of a spike in delayed discharges.
He said this was “leading to logjam right the way through inpatient care and into accident and emergency”.
The Health Secretary said all health boards were under “extreme pressure” due to the pandemic.
Extra funding of £10 million had been announced last month to help health boards with staffing, he said.
Mr Yousaf said: “There are some Edinburgh-specific issues, that’s why I meet with Edinburgh every single week, because I’m really concerned about the level of delayed discharges.
“(These are) the highest in the country.”
There is a severe lack of in-house provision in both care home and care-at-home settings, he said, while there are also challenges with the workforce.
MSP Dr Sandesh Gulhane asked the Health Secretary when the level of delayed discharges was expected to come down.
Mr Yousaf said there had been a reduction in the figures in the most recent week though numbers were still “far too high”.