Preliminary results figures for the 2022/23 Holyrood budget showed £46.9bn spent out of a possible £47.1bn.
Public Finance Minister Tom Arthur told MSPs the difference of £244m represented 0.5 per cent of the budget and would be carried over to 2023/24 spending.
The underspending was significantly less than last year when it was £650m.
The Scottish Tories said people were still “shocked” by the new figures.
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Presenting the 2022-23 budget statement in December 2021, then-SNP Treasury Secretary Kate Forbes said she received “significantly less” from the Treasury Department compared to the previous year because Covid funding had been withdrawn.
She said: “It means that the budget cannot provide the resources that all our partners want and I want to be clear: there are areas where I would have liked to have gone further.”
Mr Arthur also said today that the purchasing power of the 2022/23 budget had been “significantly weakened” by inflation and the UK government had “taken no action” to deal with it.
“We are constrained by the UK government’s spending decisions and have limited fiscal leverage, notably no ability to borrow for everyday expenses,” he said.
Still, he said the Scottish Government had invested heavily in public services.
These included an extra £900m in public sector collective agreements, almost £4.1bn in decentralized benefits, a £20m fuel insecurity fund and £216m to support 24,000 Ukrainian refugees.
He said: “We find ourselves in the most difficult financial situation since decentralization as the ongoing impact of austerity measures, Brexit and the pandemic, combined with high inflation and war in Ukraine, are putting extreme pressure on public finances.”
“Despite these challenges, we continue to manage Scotland’s finances prudently while delivering the wide range of quality public services that people expect.”
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He added: “The remaining budget of £244m, representing 0.5% of our total budget, will be transferred in full via the Scotland Reserve subject to confirmation in the final settlement.”
“It is made up of £180.6m in tax revenue, £24.7m in capital and £39m in financial transactions. There will be no loss of purchasing power for the Scottish Government as a result of this transfer.”
Tory MP Douglas Lumsden said: “The public will be shocked to learn that the SNP government, which has imposed drastic cuts in public services, went under its budget by almost £250m last year.”
“It seems that the government is happy to announce high spending figures in its budget in key areas, but has been poor in execution. Ministers say what they want, but they cannot follow their words with deeds.
“At a time when swimming pools, libraries and sports fields are being closed in our communities, it makes no sense.
“This government is talking about a skills crisis, and yet the underspending of the education and skills budget is enormous.
“Ministers claim that tackling climate change is also a key priority, but the net-zero emissions and transport budget have again been massively under-spent.
“Instead of subterfuge and quibbling, we need an explanation as to why a government that constantly complains about Westminster’s underfunding is not making full use of the resources at its disposal.”