The organisation took 63 year-old Daniel Bonventre into custody as part of its investigation into Bernard Madoff Investment Securities.
Mr Madoff, the 71 year-old head of the business, is currently serving a 150-year sentence after pleading guilty to leading the largest Ponzi scheme to have ever been set up.
He is thought to have made $65 billion from the decade-long fraud.
Mr Bonventre, the former employee of Mr Madoff will become the sixth individual to face criminal charges in connection with the case.
Securities Investor Protection Corp (SIPC) is currently working on liquidating the assets of the business to reclaim money stolen from investors.
Meanwhile, Bloomberg reported that three investors in the business have launched a separate law suit against the SIPC.
The legal action claims that SIPC president Stephen Harbeck and its directors have failed to award some claimants as much as $500,000 and are committing acts of fraud in the process.
However, Mr Harbeck denied the allegations stating that attorneys were looking to take advantage of âthe plight of these victims to incorrectly direct their anger and frustration at SIPCâ.
âSadly, this frivolous litigation will have the effect of making it harder for SIPC to focus all of its time and attention on aiding the Madoff victims,â he concluded.
By Jim Ottewill