LONDON--Indonesian coal miner Bumi PLC (BUMI.LN) said Wednesday it's finalizing the details of a separation deal with its major shareholder and co-founder, the Bakrie Group, that would result in Bumi selling its stake in Indonesia's largest coal miner, PT Bumi Resources TBk (BUMI.JK), for more than $500 million in cash to the Bakrie Group.

This marks a departure from a preliminary agreement between the two parties in which Bumi had agreed to sell a 29.2% stake in Bumi Resources for $278 million in cash to the Bakrie Group and the cancellation of the Bakrie Group's 23.8% stake in Bumi PLC.

Bumi said that it "has been made aware" that PT Borneo Lumbung Energi & Metal, Tbk (BORN.JK), which is controlled by Bumi's chairman Samin Tan and owns a 23.8% stake in Bumi, is holding ongoing discussions with the Bakrie Group to purchase the Bakrie Group's stake in Bumi. Bumi said it isn't party to those discussions but has been informed that the Bakrie Group will only sell its Bumi shares to Borneo if Bumi agrees to sell its Bumi Resources stake to the Bakrie Group.

"The separation transaction is subject to ongoing negotiations but the economic terms remain consistent with the original proposal received by the company from the Bakrie Group in October 2012," Bumi said in a statement.

The Bakrie Group has been seeking to separate itself from the troubled miner since October after repeated boardroom rifts over corporate governance issues and the launch of an independent probe into financial irregularities at Bumi's Indonesian assets. This, alongside falling coal prices, has caused Bumi's share price to plummet 82% since its initial listing as Vallar in 2010.

Bumi and the Bakrie Group signed a preliminary separation agreement in February. As part of that deal, the Indonesian conglomerate controlled by the influential Bakrie family agreed to buy an 18.9% stake in Bumi Resources from Bumi for $278 million in cash. In a second transaction, the Bakrie Group would buy Bumi's 10.3% stake in Bumi Resources in exchange for cancellation of the Bakrie Group's Bumi shares.

For the new deal to go ahead, Bumi has been informed that its shareholders would have to vote in favor of a waiver that would allow Borneo to double its holding in Bumi PLC without triggering a U.K. takeover requirement to make a full takeover offer for the London-listed miner.

The new deal would satisfy the goal of severing ties between the Bakrie Group and Bumi, while giving Bumi shareholders cash in hand rather than a mix of cash and Bumi shares as previously outlined in a preliminary proposal last year. It will also make Borneo the largest shareholder in Bumi.

Bumi said given the potential for a conflict of interest, Bumi's board directors who are affiliated with Borneo--namely Mr. Tan and Borneo CEO Alex Ramlie--"have voluntarily recused themselves from the [board approval] process."

Nathaniel Rothschild, a major shareholder and co-founder of Bumi, said Tuesday that the alternative proposal "is Samin Tan's side deal: taking control without paying a premium, and denying minority shareholders the potential upside that ALL would have enjoyed equally from buying back the stake."

Mr. Rothschild called on U.K. regulators and Bumi's board to shun such behavior and once again called for Mr. Tan to step down immediately as chairman, given his conflict of interest.

Mr. Tan has previously said that he would step down as chairman once the deal with Bakrie Group is done and a new independent chairman has been selected. He also told reporters at Bumi's annual general meeting last month that there was no side deal between him and the Bakrie Group.

Write to Alex MacDonald at alex.macdonald@wsj.com

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