The 32-year-old founder and CEO of Turing Pharmaceutical made headlines in September for raising the price of Daraprim, often used to treat HIV and AIDS patients, from $13.50 per pill to $750 per pill after buying the rights to the drug.
His arrest is reportedly not related to that price increase.
Shkreli is accused of illegally taking stock from a biotechnology firm he launched in 2011 called Retrophin Inc., Bloomberg reported, and using it to pay off unrelated business debts.
Federal prosecutors allege he also conducted a complicated shell game with his shuttered hedge fund, MSMB Capital Management, the news service added. He is charged with making sham consulting agreements and secret payoffs using the firm.
In September, Shkreli's inflammatory comments on social media and in TV interviews prompted further outcry in Congress and on the presidential campaign trail. He called the price increase "a great thing for society” while berating journalists.
"He looks like a spoiled brat to me. He's a hedge fund guy. I thought it was disgusting what he did," GOP presidential front-runner Donald Trump told reporters in South Carolina.
Trump said he was particularly disturbed by the CEO's refusal to back down after a New York Times story publicized the cost increase.
"That guy is nothing. He's zero. He's nothing. He ought to be ashamed of himself," Trump said.
Updated at 7:35 a.m.