Verlyn Olson says shippers and handlers all along the line are paying steep fines for missing deadlines but railways are exempt.
Olson says he will be raising the issue and looking for other solutions when he talks with federal and provincial counterparts in the coming days.
He admits there is no magic solution to the grain backlog, but adds that shared responsibility and penalties are a good start.
Snow and cold have contributed to delays, but farmers say rail shippers are also giving oil, potash and coal a higher priority than grain.
Olson says extreme weather is a factor, but not an excuse given everyone has to plan and make allowances for the Canadian winter.
Many parts of the Prairies enjoyed a record harvest last fall, but some crops are still sitting in fields because of rail transport problems.