BILLINGS (AP) — Montana farmers struck a deal with BNSF on Thursday that will give them a say in mediating shipping disputes with the railway.

The state’s largest grain groups — Montana Farm Bureau Federation and Montana Grain Growers — gained a seat at the bargaining table during the Grain Growers’ convention in Great Falls.

‘‘This is historic,’’ said Lochiel Edwards, a wheat farmer from Big Sandy who helped negotiate the agreement.

Historically, farmers have watched from the sidelines as shipping rates were handled by railroads and the grain elevators that bought from the farmers. Federal laws regulating rail travel didn’t take into account farmers, who have had the cost of shipping passed down to them from the grain elevators.

Bruce Wright, vice president of the Montana Farm Bureau Federation, said the arrangement often made a substantial dent in farmers’ profits.

Farmers have often complained about the shipping rates, but they could do little about it because, technically, they weren’t the ones paying the bill.

Grain elevators write the check to the railroad for shipment, and in the eyes of the federal government, that meant BNSF rates could only be challenged by the elevator.

Thursday’s agreement allows a wheat or barley farmer concerned about his shipping cost to take his complaint to his farm group, the Montana Farm Bureau Federation, the Montana Grain Growers or Women Involved in Farm Economics, who then will decide whether to move forward.

Complaints will arbitrated one elevator site at a time by a panel of five grain industry experts selected by the railroad and the grain groups.

During his re-election campaign, Gov. Brian Schweitzer criticized the proposal for only mediating freight rates one elevator at a time, and suggested that grain producers had no bargaining leverage.

‘‘My question is, when we stand before BN, should we do it on one knee or both knees?,’’ he said then.

Ron De Young, director of the state Agriculture Department, called the mediation plan adopted by grain groups a piece of the puzzle and said everyone should be working for more equitable freight rates.

Kevin Kaufman, BNSF’s group vice president of agriculture products, said the railroad’s dealings with grain groups over the past four years have shown that the state’s shipping needs are unique.

In other states served by BNSF, high volumes of crops grown in single varieties make shipping much different than in Montana, where pockets of agriculture may produce not only smaller quantities of grain, but also more than one variety.

‘‘This agreement is unique,’’ Kaufman said. ‘‘Nothing exists like this in the U.S. and it’s likely to be a template for the future.’’