Farmers in the State's Wheatbelt say a decision by Brookfield Rail to close two lines of its Tier 3 grain freight lines will hurt farmers financially.

Brookfield says the lines from York to Quairading and Merredin to Trayning, will close at the end of the month, citing a lack of government investment as one of the factors in the decision.

The closure comes on the eve of this year's grain harvest, expected to be one of the largest in recent years.

Bill Cowan from the Wheatbelt Railway Retention Alliance has told the ABC many growers will be forced to send their grain to port by road, which will cost more.

"We won't be able to move our grain to port by road in a timely fashion," he said.

"In fact the last time there was a good crop, the Tier 3 lines were kept open for that reason, because the road transport couldn't shift all the grain."

Mr Cowan said it could mean that farmers might not get their grain to the ports.

"The worst case scenario is that some of this grain will have to stand in the fields until the local bins are actually emptied."

He said it is the first time in six years that some farmers will harvest a decent crop.

"Everyone is suffering financially and if we can get this crop off, it makes a lot of money for this State and it will get a lot of farmers out of trouble," he said.

"The [road] safety and the cost to local government authorities is horrendous, and even the things that annoy us, is to fix these roads up costs more than what the rail costs anyway.

"Everyone used to say this was a no-brainer but the only people that couldn't see it was the government."

A statement from the office of the Transport Minister Troy Buswell said: "It is up to Brookfield and CBH to come to a commercial decision to keep Tier 3 lines operational, if economically viable.

"These lines only transport eight per cent of the grain freight. CBH and Brookfield may reach a mutually agreeable decision by the end of October to keep the remaining lines operational."