J. Ezra Merkin, a New York financier, wrote his investors last month that he too was shocked by the news that Bernard Madoff's hedge fund was an elaborate Ponzi scheme.

But not everyone sees him as a victim. The New York attorney general, Andrew Cuomo, has issued subpoenas in an effort to determine whether Merkin had defrauded universities and charities when he invested their money with Madoff, a person with knowledge of the case said Thursday.

Cuomo's office is seeking information from Merkin, the three investment funds that he operated and 15 nonprofit institutions that gave him money to manage. Many of the institutions are now suing Merkin, claiming that they lost millions of dollars when he had invested money with Madoff without telling them.

The person with knowledge of the case said the investigation would examine whether Merkin had properly disclosed where the money was being invested. The institutions are being asked how they were affected by the Madoff scandal. The subpoenas were issued Wednesday night.

A lawyer for Merkin, Andrew Levander, said, "We will fully cooperate with any investigation by the New York attorney general's office.

"I'm astonished," said Mortimer Zuckerman, the publisher and real estate executive whose charitable trust lost $30 million through Merkin. "Frankly, I was absolutely hoodwinked."

Today, say those who know him, Merkin is keeping a low profile. He still attends services at the Fifth Avenue Synagogue, where he is president. But he is rarely seen outside his office and home, both on Park Avenue. He has either resigned from — or been asked to leave — many of the boards on which he served.

New York University is suing Merkin over $24 million it lost. The university's chief investment officer rejected a suggestion last October by Merkin, who managed part of its endowment, that it invest in a Madoff fund. But, unknown to the university, Merkin had been investing its money with Madoff for at least eight years.

New York Law School has filed suit over a $3 million loss. Tufts University is facing a $20 million loss. Other victims include Yeshiva University, where Merkin was a trustee and headed the investment committee. Yeshiva lost $110 million of the money invested with him.

Marc Rich, the financier who was pardoned by President Bill Clinton, lost $10 million to $15 million. And Bard College, where Merkin sat on a board, estimates losses of $11 million.

They blame Merkin at least as much as Madoff.

"This has been a terrible shock," said Leon Botstein, president of Bard College. "When I first read about Bernie Madoff, I thought, 'He's not part of our team.' Back then I had no idea that somehow we would be caught up in that."

Merkin was named to the board of the Levy Economics Institute at Bard College on the recommendation of Leon Levy himself, a legendary Wall Street financier and philanthropist who died in 2003. When Yeshiva University expressed concerns over possible conflicts about investing with Merkin since he was a trustee, Ira Millstein, the respected corporate governance lawyer, blessed the relationship so long as it was disclosed.

And the offering prospectuses for Merkin's funds gave few clues. In nearly all cases, there was no mention of Madoff, just a diverse range of commonplace investments.

One mention of Madoff is in the Ascot fund prospectus, which was entirely invested with Madoff. But it does not cite Madoff as a money manager. Instead, he was listed as one of two brokers — the other was Morgan Stanley — that would clear Ascot trades.

Merkin's lineage provided him with a remarkable calling card. His father, Hermann Merkin, who fled Nazi Germany, made a fortune in the shipping business and became a major figure in New York's Jewish philanthropic elite. The elder Merkin was the founding president of the Fifth Avenue Synagogue, a center of modern Orthodox Judaism, and gave millions to help build Yeshiva University and the Merkin Concert Hall near Lincoln Center.

Ezra Merkin's address is 740 Park Avenue, the celebrated cooperative building where Jacqueline Kennedy grew up and John D. Rockefeller once lived. More recently it has been home to financiers like Ronald Perelman, Saul Steinberg, Henry Kravis and Stephen Schwarzman.

His 18-room duplex contained one of the largest private collections of Mark Rothko's large abstract paintings, valued at over $150 million.

Merkin, a graduate of Columbia University and Harvard Law School, has been described as being brusque in public, but devoted to his family in private.

"He was a member of the social elite of New York, so he was attractive to be on the board of a think tank," said Dimitri Papadimitriou, president of the Levy Economics Institute at Bard. "There was certainly no concern that there was any negligence."

Another important connection for Merkin was Stephen Feinberg, head of Cerberus Capital Management, a private investment fund with big stakes in Chrysler and GMAC, the financing arm of General Motors.

Merkin became an investor in Cerberus and put money from Merkin funds into Cerberus and its portfolio companies. For instance, his Gabriel fund invested $79 million in Chrysler, $66 million in GMAC and $67 million in Cerberus partnerships, according to year-end statements. In 2006, Cerberus appointed Merkin as nonexecutive chairman of GMAC, a position Merkin recently resigned.

Merkin's financial empire was built in large part by his management fees: 1 percent to 1.5 percent of the $5 billion in assets under management. In 2007, for instance, Merkin collected $28 million from the Ascot fund and another $12 million from the Gabriel fund.

But because Merkin is a general partner in his funds, his assets are now at risk. Should his clients prevail in court, all Merkin's assets — including his art collection and apartment — can be used to settle claims, which are estimated at $2 billion.

"If even only a few of the lawsuits are successful, the defendant, Merkin, will likely be rendered insolvent," lawyers for NYU said in a court filing. Harry Susman, an lawyer representing Merkin investors, added: "Unless he has a good explanation, he will have people after him for a long time in the future."

Zachery Kouwe and Alison Leigh Cowan contributed reporting.