The Scottish government was not adequately prepared for the Covid-19 pandemic, according to a new report by the public spending watchdog.

An Audit Scotland report said ministers had been expecting and planning for a pandemic but had based their preparations on flu.

Watchdogs also found the government acted quickly to prevent the NHS from being overwhelmed by coronavirus.

Health Secretary Jeane Freeman said the report would be considered carefully.

It is estimated the pandemic will cost the NHS £1.67bn in 2020/21 alone.

The knock-on effects mean there is a “substantial backlog of patients” waiting to be seen in the NHS, according to Audit Scotland.

The spending watchdog found that despite a number of pandemic planning exercises, not all the actions identified in these projects were fully implemented.

These included measures to ensure access to enough personal protective equipment (PPE) and to quickly address social care capacity.

Stephen Boyle, auditor general for Scotland, praised the “extraordinary commitment” of NHS staff but said the pandemic had “highlighted the need to deal with long-standing health inequalities”.

He added: “There are clear lessons to be learned from the pandemic, both in how the country could have been better prepared and in the innovation that we’ve seen.

“It’s essential that these advances are now retained and built upon.

“Getting the full range of health services back up-and-running will be challenging.”

Scotland’s initial response to Covid-19 was based on preparations for a major influenza pandemic, with three government training exercises carried out in the past five years.

But the Audit Scotland report concludes the Scottish government was “slow” at implementing the recommended improvements from the simulations in some of the areas that would become a “significant challenge” during the pandemic response.

The report states that the Scottish government “could have been better prepared to respond to the Covid-19 pandemic” and lessons must be learned.

However, auditors also found that actions, such as cancelling non-urgent operations and increasing intensive care capacity, stopped the NHS from being overwhelmed in the first wave of Covid.

Dr Lewis Morrison, chairman of the BMA Scotland, said: “There is obviously some concern that the Scottish government could have been better prepared and acted quicker on learning from various planning exercises.

“This would seem particularly true on doctors’ experiences of PPE – where early concerns needed to be rapidly addressed.

“It is concerning that the existing financial and operational challenges in the NHS have since been exacerbated by Covid – particularly given how serious the warnings from Audit Scotland have been in previous reports.”

Dr Morrison said that restarting normal levels of NHS services was going to be a “substantial challenge”.

Covid has caused or contributed to the deaths of about 9,000 people in Scotland so far, with those from the most deprived areas or ethnic minorities among the worst affected.

The forecasted £1.67bn cost of Covid in 2020/21 includes £324.5m on PPE and a near 10% rise in staffing costs.

Responding to the report, the Royal College of Nursing (RCN) said lessons needed to be learned and the “immense pressure” staff had faced over the sustained period should be fully recognised.

Director Susan Aitkenhead said: “We know nursing staff continue to be concerned about their own and their colleagues’ wellbeing and the potential long-term risks to their physical and mental health, including PTSD and long Covid.

“Going forward we need to address the opportunities to work differently and the first-hand learning and experience of nursing staff and their colleagues across health and social care must be at the heart of this.”

Health Secretary Jeane Freeman said the report’s findings would be considered carefully and highlighted the rapid increase in intensive care capacity, the completion of NHS Louisa Jordan within three weeks and the continuous operation of emergency, urgent and trauma services during the pandemic.

She said: “At no point has our NHS been overwhelmed, which is testament to swift action and extraordinary efforts of everyone involved.

“At all times the Scottish government’s actions have been guided by the best and most up-to-date scientific and medical advice. Our approach to protecting our NHS and saving lives has been constantly adapted over the past 12 months, in line with this advice and the latest scientific evidence, and these lessons will inform future pandemic planning.

“Our focus now remains on suppressing Covid-19 to the lowest possible level in Scotland, to protect our health and care services, and the people of Scotland while the vaccine is delivered as quickly and as safely as possible.”

The government was expecting a pandemic.

It had rehearsed scenarios, carried out table-top exercises and simulations, all of which identified the need to better prepare care homes and to improve stockpiles of PPE.

And despite assessing a flu pandemic as a high risk, the government did not identify it as a stand-alone factor when considering the biggest challenges to the health service.

Scotland is not alone in being caught off guard, and the report points to some of the things that went well.

Speedily increasing the capacity of intensive care and hospital beds for example, and rapidly rolling out the use of digital technology.

But this is the first time we’ve seen in black and white from an independent body that there were shortcomings in the preparations.

A public inquiry will later look at whether the decisions that were made could have led to better outcomes.