The miner and trader operates ten coal mines in the Hunter Valley in New South Wales, with little alternative other than to export coal through Newcastle.
After a period of arbitration, The Australian Competition and Consumer Commission has ruled that Glencore should pay A$0.61 per ton gross on ships carrying its coal compared to A$0.76 a ton now.
Newcastle, which is the world's largest coal port, wanted a rise to A$1.36 a ton to reflect dredging costs, while Glencore argued the price should be cut to A$0.41.
The new price will be backdated until 2016.
Glencore’s Australian coal operations contributed almost US$4bn of sales in its latest half-year or almost 10% of group revenue.