The Church of Jesus Christ of Latter-day Saints and a nonprofit entity that it controlled have been fined $5 million by the Securities and Exchange Commission over accusations that the religious institution failed to properly disclose its investment holdings.

In an order released Tuesday, the SEC alleged that the church illicitly hid its investments and their management behind multiple shell companies from 1997 to 2019. In doing so, it failed to disclose the size of the church’s equity portfolio to the SEC and the public.

The church was concerned that disclosure of the assets in the name of the nonprofit entity, called Ensign Peak Advisors, which manages the church’s investments, would lead to negative consequences in light of the size of the church’s portfolio, the SEC said.

The revelation of the illicit shell company structure dates back to 2018, when a group formerly called MormonLeaks and now known as the Truth and Transparency Foundation alleged that the extent of the church’s investments had reached $32 billion that year.

The following year, a whistleblower filed a complaint to the Internal Revenue Service, according to a 2020 Wall Street Journal report; that year, the newspaper said the church’s holdings had grown to $100 billion.

“For more than half a century, the Mormon Church quietly built one of the world’s largest investment funds,” the Journal said. “Almost no one outside the church knew about it.”

The SEC accused the church Tuesday of going to “great lengths” to avoid disclosing its investments and, in doing so, “depriving the commission and the investing public of accurate market information.”

“The requirement to file timely and accurate information on Forms 13F applies to all institutional investment managers, including non-profit and charitable organizations,” said Gurbir S. Grewal, director of the SEC’s Division of Enforcement, in a statement.

In a statement, the church said that, starting in 2000, its Ensign Peak investment management group “received and relied upon legal counsel regarding how to comply with its reporting obligations while attempting to maintain the privacy of the portfolio.”

As a result, it said, Ensign Peak established “separate companies” that each filed required disclosure forms, instead of a single aggregated filing.

“Ensign Peak and the Church believe that all securities required to be reported were included in the filings by the separate companies,” it said.

After the SEC expressed concern about Ensign Peak’s reporting approach in June 2019, the church said, Ensign Peak “adjusted its approach and began filing a single aggregated report.”

Since that time, the church said, it had filed 13 quarterly reports in accordance with SEC requirements.

“This settlement relates to how the forms were filed previously,” the church said. “Ensign Peak and the Church have cooperated with the government over a period of time as we sought resolution. We affirm our commitment to comply with the law, regret mistakes made, and now consider this matter closed.”