It's alleged the men, who know each other, set up or acquired businesses as disability providers before going on to submit false claims for NDIS services that were never provided.
The Australian Federal Police carried out search warrants under the government's anti-fraud task force across three separate homes in Western Sydney on Tuesday morning.
NDIS Minister Bill Shorten said he was determined to hold people accountable for ripping off the scheme after admitting fraud was a "big problem".
"There's nothing worse than stealing from taxpayers and people with disabilities," he told the ABC.
"For the few service providers who are cheating the system, just don't.
"I'm confident that if we can reduce some of the fraud, then we will see the scheme looking healthier financially, and that people with severe and profound disabilities are not vulnerable."
Mr Shorten said people defrauding the system would eventually be caught out, with the government determined to "clean up the name of the NDIS".
One man was arrested and charged while the other two were issued court attendance notices for offences including obtaining financial gain by deception, and dealing in proceeds of crime.
The man who was arrested was granted conditional bail and will face court on April 4, while the other two will appear on March 21.
Anyone with information about suspected fraud should contact the NDIS fraud reporting and scams helpline on 1800 650 717.
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