A secret deal for the Western Australian Government to get a slice of Brookfield Rail’s grain profits has been revealed.

Brookfield Rail holds an exclusive lease over several state-owned lines, shifting product primarily for CBH group.

It is not known how much the State Government would have made from the clandestine arrangement, which would have run for the next nine years if it had been successful.

Documents showing the contract clauses in a deal between the WA Public Transport Authority and Brookfield have been exposed by a WA Parliamentary committee, which was looking into the management of the state's grain freight network.

Reports say that CBH pays around $50 million each year for access to the rail network, but has been locked in a dispute with Brookfield over future lines and long-term access to existing ones.

A spokesperson for CBH, a grower-owned co-operative, said the revelation had shown why the company found it so difficult to reach a rail access resolution.

“We’d certainly be really interested to hear from government about how they’re managing what could be perceived as a conflict of interest, where the department that’s responsible for protecting the access seeker and managing the access code is also profit-sharing with the operator,” David Capper, CBH general manager of operations, told the ABC.

“We’ve heard a lot about his being an issue for CBH and Brookfield to resolve.

“I think now we can understand that that is no longer the case. There are other people involved and need to assist in bringing it to a resolution,” he said.