But she pledged a vote for independence in next month's referendum would halt the change, preventing "truly horrifying cuts in support for disabled people".
At the moment some 190,000 people in Scotland receive support from the Disability Living Allowance (DLA) which is being replaced with the Personal Independent Payment (PIP) as part of the UK Government's programme of welfare reform.
This will result in more than 100,000 Scots losing some or all of their disability benefits, according to the Scottish Government.
A report looking at the impact of the changes said that these people lose at least £1,120 a year, but added that almost 50,000 people receiving the enhanced weekly mobility allowance to help them get about could lose between £1,820 and £2,964 a year.
Conservative welfare spokesman Alex Johnstone accused the Deputy First Minister of trying to frighten disabled people in the run up to next month's vote on independence.
The Tory MSP told BBC Radio Scotland: "What Nicola Sturgeon is trying to do is raise the level of rhetoric and try to frighten some people in the build up to the referendum.
"It is simply not the case that people will be harmed in the way she is describing."
Ms Sturgeon, however, insisted: "It is simply wrong that so many disabled people in Scotland are set to lose so much money as a result of these UK Government changes.
"I am particularly concerned that the redrawn mobility rules will mean that almost 50,000 people will lose entitlement to up to £3,000 per annum. These are truly horrifying cuts in support for disabled people."
She added: "This analysis of the UK Government's welfare changes underlines the pressing need for a Scottish welfare system that has, at its heart, the clear principles of fairness and dignity.
"Following a vote for independence, we will halt the abolition of DLA in Scotland and its replacement by PIP."
Mr Johnstone argued that 90,000 disabled Scots could be better off as a result of the reforms.
He told the Good Morning Scotland programme: "What is happening with the change is we are trying to priorities those who need support most. Nicola Sturgeon's own figures say 100,000 of 190,000 will lose some or all - I might dispute that - but these figures demonstrate that 90,000 people will actually see their benefits increase as a result of these changes."
He added: "The 100,0000 she is quoting is a slight misrepresentation, some of these people will find their way back on to out of work benefits, and she's not including them, so if you lose your disability benefits and go back on to an out of work benefits while you are looking for work, you will be supported, but through a different allowance."
Mr Johnstone continued: "Sadly over successive governments we have had the habit of massaging the unemployment figures by putting people onto disability allowances and leaving them there on the scrap heap for a whole generation at a time. We can't allow that to happen.
"We need to ensure people who are able to work are put back into the work process as early as possible."
The Scottish Government report on the impact of welfare reforms warned that disabled people "are likely to experience significant loss of income" as a result of the changes.
The 190,000 people receiving DLA in Scotland will be reassessed before 2018 to determine if they are eligible for the new PIP, but the report stated: "Of these, it is expected that a total of around 105,000 working-age disabled people will lose some or all their disability benefits by 2018, with likely a loss of at least £1,120 per year.
"Of this number around 47% (49,000) of reassessed DLA claimants will get no PIP award and the remaining 53% (56,000) will face a reduced PIP award."
The report estimated that the introduction of the PIP would "lead to a total reduction in spending of £740 million between 2013/14 and 2017/18 with expenditure being reduced more substantially in the later years, and by £310 million per year by 2017/18".
It also pointed out that Scotland has "higher levels of long-term health problems and disability compared with the UK as a whole", with the 2011 census finding 20% of Scots had reported long-term health problems or disabilities, compared with 18% of people in the UK as a whole.