Western Australia's grain rail transport system is at a standstill for the first time in the industry's history, with the CBH Group and Brookfield Rail unable to finalise an interim rail access agreement.

The state's main grain handler and the rail company, which has an exclusive lease over the state's grain rail network, cannot agree on price and other conditions necessary to finalise a deal.

The current agreement expired at midnight on Thursday, April 30 and despite long negotiations into the night a deal was not struck.

As a result CBH is required to park its rail fleet at various sites around the state.

CBH Group CEO Dr Andy Crane said the situation was difficult to manage, especially while it was busy.

"We are close to a peak period, harvest is peak for growers but out-loading is peak for CBH all year round," Dr Crane said.

"Currently at the moment customers are looking for incredibly large flows of grain to port.

"The reputation of the state as a secure origin of grain is being damaged by the loss of this export pathway to our growers."

Dr Crane said contingency plans were being prepared.

"Contingency plans will be trucks, but fundamentally that is not what you would plan for, normally you would have assured access to a track to run trains on so these are very unusual circumstances," he said.

Brookfield Rail CEO Paul Larsen said he was confident a deal could still be reached.

"I'd say the negotiations have been professional and courteous and without doubt both the guys at CBH and the guys at Brookfield are both putting in the big hours and burning the midnight oil and working with each other to try and get a deal done."