WASHINGTON — The Church of Jesus Christ of Latter-day Saints, the leading Mormon denomination, and a nonprofit operating under it will pay $5 million to settle Securities and Exchange Commission charges that the church failed to disclose its relationship to shell companies.

The SEC’s order said Ensign Peak Advisers Inc., the Utah-based nonprofit that manages the church’s investments, hid the size of the church’s equity portfolio under 13 limited liability companies — including 12 “clone LLCs” — from 1997 through 2019.

The nonprofit also failed to file Forms 13F, which are required to disclose the value of certain securities overseen by investment managers, according to the SEC. The forms were filed in the name of the shell companies, instead of Ensign Peak Advisers. The agency said the records also misstated that the LLCs had sole investment and voting discretion over the securities, which the nonprofit really controlled.

The SEC said the church’s concern over negative public reaction to the disclosure of its vast investment portfolio, which reached $32 billion in value in 2018, prompted the steps to mask its holdings.

Ensign Peak Advisers agreed to pay a $4 million penalty to the SEC, while the church agreed to pay $1 million, the agency said.

“We allege that the LDS Church’s investment manager, with the Church’s knowledge, went to great lengths to avoid disclosing the Church’s investments, depriving the Commission and the investing public of accurate market information,” Gurbir Grewal, director of the SEC’s Division of Enforcement, said in a statement. “The requirement to file timely and accurate information on Forms 13F applies to all institutional investment managers, including non-profit and charitable organizations.”

The Church of Jesus Christ of Latter-day Saints told CNBC that it “cooperated with the government” and considers “this matter closed.”

“Since 2000, Ensign Peak 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, Ensign Peak established separate companies (LLCs) that each filed Forms 13F 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,” Chris Moore, a church spokesperson, told CNBC.

“This settlement relates to how the forms were filed previously. Ensign Peak and the Church have cooperated with the government over a period of time as we sought resolution,” Moore added.

— CNBC’s Jim Forkin contributed to this story.