By Liz Hoffman 

Freeport-McMoRan Inc. is nearing a settlement of more than $100 million to resolve allegations its board and executives had conflicts of interest while negotiating the natural-resource company's $9 billion purchase of two affiliates last year, according to people familiar with the matter.

The agreement would resolve a lawsuit filed by some of Freeport's shareholders alleging that the company overpaid when it bought McMoRan Exploration Co. and Plains Exploration & Production Co. The shareholders allege that the deals were an effort to rescue a struggling McMoRan, in which Freeport, its board members and key executives owned shares.

Neither Freeport, nor its directors or executives, is expected to admit wrongdoing as part of a settlement, which would come in lieu of a trial.

Under the preliminary settlement agreement the parties have reached, Freeport would pay more than $130 million, with much of that earmarked for a special dividend for its shareholders, some of the people said. After legal fees and other costs, the dividend would likely amount to more than $100 million, or 10 cents per Freeport share, those people said.

The settlement and the payout to shareholders would be among the largest in a recent string of high-profile victories in litigation over merger deals, which has become a common battleground between companies and their investors. It could also serve as a warning for companies contemplating complicated takeover transactions involving multiple, overlapping constituencies.

Freeport agreed in December 2012 to pay $6.9 billion in cash and stock for Plains, a Houston-based oil-and-gas producer, and $2.1 billion in cash for McMoRan, a Louisiana rival in the business. For Freeport, then one of the world's biggest publicly traded copper miners, the moves were a return to the oil-and-gas business after splitting from McMoRan in the 1990s. The takeovers created a global company with a market value of roughly $30 billion, producing commodities including oil, gas, copper and gold.

But ties between the three companies, including overlapping board members and ownership stakes, led to claims that Freeport had used the veil of a strategic acquisition to bail out McMoRan, a key premise of the lawsuit.

Shareholders also alleged that, to seal the deal, Freeport also swallowed Plains, which had veto power over the McMoRan transaction.

Freeport had agreed to pay a 74% premium for McMoRan, whose shares had tumbled amid delays and other problems with its flagship Gulf of Mexico oil well.

Freeport owned preferred shares representing 16% of McMoRan, and the two companies also shared six directors, a relic of their combined past. McMoRan's chief executive officer, James "Jim Bob" Moffett, was also Freeport's chairman, and Freeport's CEO, Richard Adkerson, was McMoRan's co-chairman and former CEO. Nine Freeport directors owned about 6% of McMoRan stock between them, according to court and regulatory filings.

Plains, meanwhile, owned 31% of McMoRan, shares it had received when it sold McMoRan a portfolio of shallow-water offshore acreage in 2010. Under McMoRan's charter, Plains' stake was large enough to block a sale of McMoRan to an unwanted suitor.

Investors sent Freeport's shares down 20% over the two days following the announcement of the deals, and some, including BlackRock and T. Rowe Price Inc., publicly raised concerns about potential conflicts of interest. On a conference call after the deals were announced, a BlackRock Inc. managing director said to Freeport executives, "I presume that everybody on the call from your side is conflicted because of the various different roles."

The transactions closed in June and July 2013, after both Freeport and Plains agreed to issue special dividends of $1 and $3 a share, respectively.

Freeport's shares climbed about 35% through July, but, like other energy stocks, have been hit hard in recent months by falling oil prices.

Most of the cost of the settlement would be paid for using a special type of corporate insurance policy that covers directors and executives, according to some of the people. Freeport would pay for the rest.

Investors routinely challenge takeovers in court now, but the overwhelming majority of cases are settled after companies agree to pay fees to plaintiffs' lawyers and to disclose more information or make minor changes to deal terms. These fees only averaged about $500,000 last year, according to Cornerstone Research.

But shareholders have scored a few notable successes lately. In October, a judge ordered RBC Capital Markets LLC to pay $76 million to shareholders of an emergency-services company whose buyout the firm advised on in 2011. RBC has said it plans to appeal.

In June, private-equity giant KKR & Co. agreed to pay $29 million to settle allegations that it shortchanged investors in its acquisition last year of industrial-machinery maker Gardner Denver Inc.

Write to Liz Hoffman at liz.hoffman@wsj.com

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