Xstrata is buying the Prodeco Coal Mine in Columbia.

Leading shareholders in Xstrata are threatening to vote against a $6 billion (£4.2 billion) rights issue after the Anglo-Swiss miner signed a separate “sweetheart” deal with its largest investor.

The heavily discounted issue will see shareholders offered two new shares priced at 210p for every existing share — a 66 per cent reduction on Wednesday's share price.

However, Glencore, the Swiss commodities trader that owns 34.5 per cent of Xstrata, will effectively dodge the rights issue. Xstrata will instead buy the Prodeco coalmine in Colombia from Glencore with $2 billion of cash raised from the rights issue. Glencore will have the right to buy back the mine a year later for $2.25 billion.

Shareholders told The Times that they were concerned by the preferential treatment that Glencore appeared to be receiving, as well as the valuation of the Prodeco mine. They also questioned Xstrata's decision to buy the mine while announcing $3 billion of capital expenditure cuts this year because of falling commodity prices.

Xstrata said yesterday that the mine's audited results showed a profit last year of only $41 million, implying a takeover premium of 45 times earnings. However, the company insisted that the figures were not an accurate reflection of the mine's profitability. Xstrata's guidance indicated earnings of about $400 million, although as a privately held asset within Glencore, a private company, there is no evidence to support this valuation.

One major shareholder said: “I think the corporate governance of this company is shocking. Heads have to roll. The board of Xstrata are only listening to one third of their shareholders. This deal is clearly highlighting that there is a concern about the financial condition of Glencore. The rest of the market is being asked to pay for it.” Another investor said: “This deal should not be accepted as it stands.” A fund manager added: “This smells pretty fishy. The whole deal is pretty suspect both on valuation and in terms of Glencore's role.”

The shareholders have threatened to vote against the rights issue in March. Mick Davis, Xstrata's chief executive, insisted that it was a good deal. He said: “Glencore's ongoing support has provided Xstrata with an opportunity to acquire Glencore's world-class, cash-generative Prodeco coal operations for $2 billion.” Shares in Xstrata, which announced earnings before tax last year down 17 per cent, closed up 22 and half p at 645½p.