The Federal Government has knocked back an application by one of the world's biggest mining companies to have the Port of Newcastle regulated by the national competition watchdog.

The port was purchased by a consortium for $1.75 billion in May 2014.

Glencore said the new operator has since increased prices for coal ships using the shipping channels by around 60 per cent, and said it has been told by the New South Wales Government there is no form of control over such increases.

The company applied to the National Competition Council (NCC) to get access to the port's shipping channels for at least the next 15 years.

It would mean third parties could use the nationally significant facilities, and the Australian Competition and Consumer Commission could intervene in pricing disputes.

In its application, Glencore said "apart from the cost increases themselves, this provides no certainty in relation to the scale or nature of future cost increases".

"It therefore creates commercial risks for current and future coal projects in the Hunter Valley, and dependent operations in relevant associated upstream and downstream export and mining services.

"The uncertainty associated with the lack of regulatory oversight over future port pricing at the Port of Newcastle is likely to have a particularly profound impact on marginal mining operations, given the resources downturn and increased uncertainty surrounding the global price of coal".

But the Finance Minister and Acting Treasurer Mathias Cormann has denied Glencore's application, in accordance with the NCC's recommendation.

He said he is "not satisfied that access to the shipping channels will promote a material increase in competition in any dependent markets".