Tory leader Douglas Ross also claims that victims of crime support is also falling, despite a record £41 billion package being set out by finance secretary Kate Forbes at Holyrood.
But a spokesman for the SNP minister said her budget was set in the face of a 5% cut in capital funding from Westminster.
The budget prompted concern among businesses after Ms Forbes announced that she would only provide 100 per cent rates relief for three months, instead of the full year, as the Scottish Conservatives demanded.
This will change if UK Chancellor Rishi Sunak announces such a measure for the full year in his own budget in March.
Mr Ross said: “Despite this being the biggest ever Scottish budget, the SNP still threw in more than £400 million of sleekit, under-the-radar cuts that Kate Forbes obviously didn’t get around to mentioning yesterday.
“This budget failed to put Scotland’s recovery first by abandoning preparations for indyref2."
Analysis produced by the Tories highlights a £268m reduction in the social housing budget, while there is a combined cut of £67m across major rail public transport projects and infrastructure.
Among the other cuts being highlighted by the Tories is a £500,000 reduction in victim and witness support, while Creative Scotland and other arts funding is down by more than £4m.
The new Scottish National Investment Bank sees its funding fall by £36m to £205m, while the budget for innovation and industry is halved to £43.8m.
Mr Ross said: “Once again, business has been treated as an afterthought. The announced rates relief didn’t go far enough and we will fight for changes at future stages of the budget.
The budget will see a record £16bn invested in the NHS in Scotland, while Police Scotland was also given an additional £60m, which will wipe out its structural deficit.
A spokesperson for Ms Forbes said: “Douglas Ross should be embarrassed by the fact that he doesn’t know his own government has cut Scotland’s capital budget by more than 5 per cent this year.
“We’ve called on the UK Government to reinstate this money to ensure that Scotland’s economic recover doesn’t suffer at the hands of yet more Tory cuts.”