Seth Klarman, the hedge fund manager who has been compared with billionaire Warren Buffett, has a very large position in Puerto Rico's controversial debt, CNBC reported.

Klarman's hedge fund, Baupost, owns $911 million of the island's bonds through Decagon Holdings entities, according to a public court filing.

"The Baupost Group is a holder of COFINA [Puerto Rico Sales Tax Financing Corp.] bonds through the Decagon entities. Baupost regularly makes investments through subsidiary holding entities," a Baupost spokeswoman told CNBC.

Baupost had $30 billion in assets under management as of March 2017, according to the firm.

Puerto Rico in May announced a historic restructuring of a portion of the U.S. territory's $70 billion debt through courts after negotiations with bondholders failed. The announcement marks the biggest bankruptcy-type process ever for the U.S. municipal bond market.

Puerto Rico Gov. Ricardo Rossello at that time said that a federal control board overseeing the island's finances agreed with his request to put certain debts before a court. The U.S. territory was hit with multiple lawsuits from creditors seeking to recuperate the millions of dollars they invested in bonds issued by Puerto Rico's government, which has declared several defaults amid a 10-year recession.

Puerto Rico's bonds plunged Wednesday after President Donald Trump pledged to wipe out its debt in an interview with Fox News. The island's general obligation bonds fell to 36 cents on the dollar versus 56 cents on the dollar last month.

Two weeks ago, the island was hit by Hurricane Maria, a Category 4 storm that left most of the population without electric power.

Puerto Rico currently has more than $70 billion in debt. Cate Long, founder of Puerto Rico Clearinghouse, told CNBC in an email retail investors own about 75 percent of the island's debt.

Baupost has $30 billion of assets under management as of March 2017, according to the firm.

Klarman's fund has generated annual returns of 16.4 percent and $22.6 billion in net profit for clients since inception through 2015, according to a Morgan Creek Capital letter. Baupost's main fund posted a 'high single-digit' return last year.

The hedge fund manager has largely avoided controversy over his career and is often compared with Buffett for his disciplined investing philosophy and solid returns. As the political rhetoric heats up around what Wall Street is owed as Puerto Rico tries to recover from this tragedy, a negative spotlight could fall on owners of the controversial debt like Baupost.

That is likely something Klarman would not welcome since he is notoriously reclusive. He rarely appears publicly and used copies of his "Margin of Safety" investment book still sell for more than $700 online.

Klarman in 2015 took time off after undergoing cardiac bypass surgery, according to a letter sent to the hedge fund’s investors.