Shkreli was already widely reviled because a different drug company he founded, Turing Pharmaceuticals, raised the price of a life-saving drug from $13.50 to $750 per pill. He resigned as its CEO on Friday.
Turing announced on Friday that it had appointed a new interim chief executive to replace Shkreli.
Shkreli through his press relations firm said he is confident he will be cleared of all charges, adding that some of the charges involved "complex accounting matters" that authorities failed to understand.
The verified Twitter account for Shkreli was apparently hacked over the weekend, but those tweets were deleted midday Monday, and a new message was posted.
—The Associated Press contributed to this report.