The Menzies Research Institute study was based on blood samples from 141 people with relapsing remitting MS, including some in Tasmania.
Results showed the amounts of several molecules in the blood - such as the lipids sometimes known as bad fats - were linked with disability level.
The researchers also found improving fat profiles in the blood could slow the progression of MS.
Rather than influencing the inflammatory processes which underlie relapses, the study found that fats in the blood may influence ongoing degeneration of brain tissue which drives the disease's progressive phase.
Lead researcher Dr Ingrid van der Mei said linking lipids to the progression of MS was an important finding.
"Our new findings indicate that clinicians should monitor and treat adverse lipid profiles in Australians living with MS," she said.
"That means if we are reducing those lipid levels by people improving their physical activity or improving their weight or having a better diet, that might actually influence how their disability progresses."
Dr van der Mei said the research could influence the way neurologists regard fat levels.
"They might be more proactive in terms of measuring cholesterol levels in people with MS," she said.
Researchers say the study is a highly valuable long-term data resource which provides detailed information on relapses, disability, lifestyle, genetics and other factors.
The research has been published in the Multiple Sclerosis Journal and Journal of the Neurological Sciences.