Scottish Conservative health spokesperson Dr Sandesh Gulhane said the report was a "damning indictment of the SNP's appalling mismanagement" of the NHS.
He said : "Successive SNP health secretaries have been asleep at the wheel as the health service has ended up in permanent crisis on their watch.
"Their dire workforce planning and complete lack of vision means that delayed discharge has reached record levels, hundreds of thousands of Scots are on NHS waiting lists and cancer waiting times have not been met for over a decade."
Labour health spokesperson Jackie Baillie said: "John Swinney likes to talk up his NHS record but this damning report shows the scale of SNP incompetence on his watch.
"Spending on agency staff is up 45% on five years ago, yet delayed discharge is at a record high and the NHS is missing three-quarters of waiting list targets - after 17 years of the SNP, our health service is broken."
She added: "The report shows clearly the price hard-working NHS staff and patients are paying for the lack of leadership from the SNP."
Leader of the Scottish Liberal Democrats, Alex Cole-Hamilton, said the NHS "is on its knees" due to SNP mismanagement.
“Hundreds of thousands of Scots are trapped on an NHS waiting list, while record numbers are stuck in hospital because they can’t get the care they need at home or in the community.
“With staff overwhelmed and the health and social care system going backwards on so many measures, the SNP Government must now admit that its three-year old NHS Recovery Plan has flopped," he said.
Health Secretary Neil Gray agreed that "reform is essential" for the NHS, and said ministers know people are waiting too long for treamment.
"Significant activity is under way through our £30m investment to target pandemic backlogs. This will see around 12,000 additional new outpatient appointments, around 12,000 additional inpatient/day-case procedures and over 40,000 diagnostic procedures delivered.
"This year we are providing more than £19.5bn for health and social care and under this government funding for the NHS has increased in real terms by 30%," he said.