Scottish ministers said the personal independence payment, which replaces disability living allowance, would result in thousands losing benefits.
Deputy First Minister Nicola Sturgeon said the cuts were “simply wrong”.
The UK government has said the new system would target help at those who needed it most.
The personal independence payment (PIP) is intended to help with the living costs for people aged 16 to 64 with disabilities or long-term health problems.
The Department for Work and Pensions (DWP) began a rollout of the PIP in Scotland in January. Existing claimants of the disability living allowance (DLA) have been assessed for their eligibility for the PIP.
The DWP has claimed: “The majority of existing DLA claimants won’t be re-assessed until 2015 or later, after DWP has considered the findings of the first independent review in 2014.”
The UK government’s Minister for Disabled People, Mark Harper, said: “The old DLA system was extremely outdated, with the majority of claimants getting the benefit for life without systematic checks on their condition.
“Personal Independence Payment (PIP) includes a face-to-face assessment and regular reviews to ensure support goes to those who need it most.
“We continue to spend around £50bn a year on disabled people and their services and 510,000 will actually get more under our reforms”.
The Scottish government has published a report which analyses the impact of the welfare reforms on disabled people in Scotland.
It comes ahead of a Holyrood debate on its plans for welfare in an independent Scotland.
It claimed the UK government’s policy will result in 105,000 claimants losing some or all of their benefit by 2018, cutting more than £300m a year from benefit spending.
Ms Sturgeon said she would halt the reform if Scotland voted for independence.
She told BBC Scotland’s Good Morning Scotland programme: “I want to see an independent Scotland have a welfare system that is fit for purpose but I am deeply concerned about the impact of Westminster cuts on a whole range of people, particularly on disabled people.
“We know that these cuts are hitting disabled people disproportionately and what we are publishing today is analysis showing that of the 190,000 disabled people who currently get Disability Living Allowance, as the transition to personal independence payments takes place, more than 100,000 of them will lose either all or some of their entitlement.”
She added: “Yes, we need a sustainable welfare system but is anybody really arguing, is the UK government arguing, that 100,000 of the 190,000 long-term disabled people getting help, no longer need it.”
The Scottish Conservative welfare spokesperson at Holyrood, Alex Johnstone, told Good Morning Scotland that Ms Sturgeon was “trying to frighten people in the build up to the referendum”.
He said the changes were designed to “prioritise” those who needed support most.
Mr Johnstone said: “The 100,000 which she is quoting is actually a slight misrepresentation.
“Some of these people will find their way back on to out-of-work benefits and she is not including that.
“So if you lose you disability benefit and go back on to an out-of-work benefit while you are looking for work then you will be supported but through a different allowance.”
He added: “It is essential that if we are going to pay support to people with disabilities that we know what their level of disability is and ensure that they are getting the support appropriate for the conditions they suffer.”