The UK Government has "picked the pocket of the health service" in Scotland, with funding claimed to be £55 million lower than promised.
A "disappointed" Jeane Freeman told MSPs the UK's budget allocation of the Barnett formula for health for 2019-20 fell short of what she was told Scotland would get.
The Health Secretary said the Scottish Government has made up this shortfall, putting further strain on other parts of the budget.
Ms Freeman said: "The Scottish Government has passed on resource consequentials in full and provided an additional £55 million.
"This reinstates the UK Government's reduction and protects resources for our frontline services."
The Cabinet Secretary agreed with a comment from George Adam MSP, who said: "It's almost as if Westminster has picked the pocket of the health service to the tune of £55 million."
He stressed if the shortfall had not been made up "we would have had more difficult decisions to make than we currently have".
Ms Freeman said: "The other side of that, having made good that shortfall from the overall Scottish budget in a situation where the Scottish Government's budget is significantly reduced, then that puts pressure elsewhere.
"The money has to come from somewhere. It should have come from the UK Government because that was the commitment they made. They didn't honour that commitment."
The total spending on health and sport for the next year is forecast to be in excess of £14 billion, she said to MSPs on the Health and Sport Committee, which "includes a further shift on the balance of spend towards mental health and to social and community care".
Ms Freeman also told the committee the Scottish Government was using £392 million to help reduce waiting times.
She said: "This will support our Waiting Times Improvement Plan and will lead to sustainable improvements to performance, including the aim that by 2021 95% of outpatients and 100% of inpatients will wait less than 12 weeks to be treated."
This year will also be the first when Scottish health boards will be able to spend more or less than their budget so long as they are balanced in three years.
Explaining the changes, Ms Freeman said: "In return for their efforts in delivering the reforms set out in the delivery plan and the financial framework, boards will be required to deliver a break-even position over a three-year period, rather than annually, as is the case currently.
"In every year, boards will have 1% flexibility on their annual resource budget to allow them the scope to marginally underspend or overspend in that year."
She added: "The spending plans are supported by greater flexibility to assist boards in planning beyond one year and to consider key areas of investment such as in relation to primary care, mental health and waiting times improvements."
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