By Alex MacDonald and Ian Walker

LONDON--Commodities titan Glencore PLC (GLEN.LN) said Wednesday it has agreed to sell its remaining 62.5% stake in the long-delayed and troubled $5.9 billion Philippine Tampakan copper-gold project for an undisclosed sum.

The Baar, Switzerland-based trader and producer of commodities ranging from coal, zinc, copper, oil and grains had stated as early as in 2013 its desire to exit the greenfield project, alongside other projects, since the company didn't want to spend billions of dollars developing projects from scratch that could face significant cost overruns and construction delays.

Glencore inherited a stake in the project when it acquired Anglo-Swiss miner Xstrata PLC that year. The Tampakan project is located on the southern island of Mindanao and was due to start commercial production in 2019 but has faced setbacks ranging from a provincial ban on open pit mining and difficulties in securing consent to resettle affected communities.

The project also faced allegations of funding the military in exchange for protection after the project suffered two attacks from the armed wing of the Philippines' Communist Party in 2008. Glencore said the project's operator, Sagittarius Mines Inc., provided funds at the behest of the local government and only for a community-based food, fuel and first aid program run by civilians; the death of a mining activist at the hands of the military wasn't related to Tampakan and all funds that supported the military ceased in 2013, it added.

The project is owned by SMI, a joint venture that is 37.5% owned by Australia-based Indophil Resources NL and 62.5% owned by Glencore.

Philippines-incorporated Alsons Prime Investments Corp. acquired the remaining shares it didn't already own in Indophil in January, valuing Indophil's equity at $361 million. Glencore, which owned a 13.1% stake in Indophil voted in favor of that deal.

Glencore is now seeking to sell its direct SMI stake to Alsons' Indophil to complete its exit from the project. Glencore didn't disclose the details of the agreement but said it was subject to certain conditions that must be secured before June 30.

The Tampakan project was previously forecast to be a low-cost copper and gold mine, producing an average of 375,000 tons of copper and 360,000 ounces of gold annually over its initial 17 year operating life. The mine was forecast to boost the Philippine's economic output by 1%, according to presentation on Indophil's website.

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

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