In a letter to the Health Committee, Alex Neil has highlighted that the UK Government's own assessment of the impact of its reforms could amount to a reduction in UK health spending of more than £1 billion a year.
Under the current funding system, this will result in a budget loss for Scotland, reducing the amount available to fund public services, Mr Neil said.
The NHS in England has been reformed by a series of changes set out in the Health Social Care Act.
The Health Secretary said: "The UK Government Department of Health modelled the savings it would seek from health spending through the Health and Social Care Bill's impact assessment.
"It sets out that in 2014/15, and in each following year up to 2019/20, that they projected savings of £1,068 million per annum.
"If these monies were to be removed from health spend and not otherwise used in another area which did have Barnett consequentials this could see the Scottish budget reduced by over £100 million per annum.
"While here in Scotland we have policy control over health allowing us to plot a different course which ensures the NHS in Scotland remains in public hands, it is clear that so long as our finances are set by the UK Government they can always be impacted by their policy choices."
Meanwhile, the Scottish Government has published Scotland's Future and Scotland's Health - a booklet focusing on health and independence.
Speaking as he visited the site of an administration complex for the New South Glasgow Hospital Campus, to be funded with £20 million, Mr Neil said: "The superb, flagship project to build a new South Glasgow hospital is apt demonstration of this Government's commitment and investment in Scotland's NHS.
"As Scotland's Future makes clear, all these gains would be protected under independence. In an independent Scotland we will continue to provide high-quality, world-leading health and social care to the Scottish people in a way that reflects the founding principles of our NHS."
Conservative health spokesman Jackson Carlaw said: "The Health Secretary really has to get his facts right.
"NHS spending in England is ring-fenced and the savings being targeted are for reinvestment in the NHS - there are no cuts.
"Alex Neil targets all Scottish health boards with efficiency reductions, again these are not cuts but savings which can be reinvested in Scotland's NHS.
"Lastly, there has been £1.3 billion in Barnett consequentials since 2011, which represents the entire increase over this period in Scotland's NHS spending."
The UK Government's Department of Health has said all savings would be reinvested in patient care, but a Westminster committee report has found a lack of transparency over what the cash has actually been spent on.