The billionaire investor told clients his firm was subpoenaed by prosecutors in New Jersey, according to a letter obtained by CNBC.
In the letter, Cooperman says the investigation is in very early stages and that the firm is cooperating fully. The subpoenas seek information on the trading of certain securities.
The U.S. Attorney's Office and the Securities and Exchange Commission declined comment.
Cooperman, the founder of hedge fund Omega Advisors, is one of the most respected figures in the investment business.
Cooperman's long-term track record is strong despite losses in 2014 . Omega's main fund has generated compounded annual returns of 14 percent, net of fees, since 1991, according to someone familiar with the matter. The source added that 2014 was the first year in which Omega took losses even though the S&P 500, which rose 11 percent, was up.
"We are cooperating fully with the government's request for information. There have not been any allegations of any wrongdoing at Omega. We have conducted ourselves properly at all times and are confident that when the government completes its review it will come to the same conclusion," Cooperman told CNBC.
-Lawrence Delevingne contributed to this report.