In a blog post on the Audit Scotland website Stephen Boyle said the government had been “spending at unprecedented levels” but the need to address backlogs in public services like the NHS and the courts will put further pressure on finances.
The Scottish Government has so far spent more than £9bn on the Covid-19 response, £8.6bn of which had been funded through Barnett consequentials from the UK Government, and Mr Boyle said a further £4.6bn allocated from the UK Government was not guaranteed, and could potentially fall.
Overall, he said, the Scottish Government had spent £48bn of its budget of £48.5bn last year, with the £449m underspend “banked” in the reserves to be spent in this financial year, as agreed in the budget.
“Financial pressures are both acute and unpredictable,” he said. “Alongside the costs of an ongoing public health crisis, increased spending is also needed to address backlogs in the NHS and the courts, and help education and the economy recover.
"The challenges to maintaining the long-term health of the public finances pre-date the pandemic. A continued focus on medium and long-term financial measures, alongside immediate responses, is essential.
"Managing volatility in the financial position will continue to be difficult, and pressures on the public purse may accumulate.
"Having a clear picture of how Scottish Government and UK Government initiatives are working together as the pandemic response changes is needed to properly understand the effectiveness of Covid-19 measures and to identify financial pressures. Effective communication and co-operation between governments will be central to this."
He said Audit Scotland's immediate focus would be on where pandemic money is being spent.
"Transparency over public spending also remains vital,” he said. “Covid-19 has undoubtedly made understanding the flow of public finances more complex than ever.
“We are auditing the Covid-19 spending that has taken place across public bodies. In the short term, we will assess how much has been spent, and on what. And in the longer-term we'll assess what difference that spending has made.”