The F.B.I. in New York declined to comment, citing an “ongoing investigation.”
It’s not clear how the foundation lost its tax-exempt status. It could have given it up, or it may have been taken away after an I.R.S. investigation. Eric L. Smith, a spokesman for the I.R.S., said the agency could not comment, citing federal privacy laws.
The I.R.S. can also revoke tax-exempt status if a foundation fails to file a Form 990 for three consecutive years, although that rule took effect in 2010. Steven T. Miller, a former acting I.R.S. commissioner and now the national director of tax at Alliantgroup, said Form 990s “are vital both for regulators and the general public to understand the finances of a given entity.”
The scant filings by Mr. Epstein’s foundation, he said, showed a “lack of transparency.”
And over the years, Mr. Epstein operated at least three other charities, including one based in the Virgin Islands. (Mr. Indyke, his lawyer, long served as an officer for Mr. Epstein’s charities and other businesses.)
Two of Mr. Epstein’s foundations relied on wealthy business titans to provide millions in seed capital. His C.O.U.Q. foundation received about $21 million in stock and cash from charities of Leslie H. Wexner, the billionaire retail magnate whose company owns Victoria’s Secret. Mr. Epstein’s Gratitude America foundation received a $10 million donation in 2015 from a company tied to the private equity billionaire Leon D. Black.
Mr. Epstein’s other foundations complied with federal disclosure rules, making his namesake foundation the outlier.
“It doesn’t pass the smell test,” said Mr. Sheil, the retired I.R.S. special agent.
After his 2008 conviction, Mr. Epstein took great pains to burnish his reputation — and the foundation played a key role.
In 2013, a Wikipedia user named Turvill made a number of changes to the page for the foundation. The changes included saying the foundation had given more than $200 million to a long list of notable scientists since its inception, then raised its claim further by describing that sum as its approximate annual outlay.