Mr Forrest said he was shocked to discover the site was not decommissioned after Wimmera Container Line moved operations to the Wimmera Intermodal Freight Terminal at Dooen in September.

"I feel a bit culpable because I worked my butt off to get the funding to get the trucks out of the city," he said.

"Somebody has let me down by not exercising due diligence over the Mill Street terminal.

"Something has gone badly wrong that procedures were not put in place to decommission that site.

"It is a complicated mess, frankly."

Mr Forrest would not say who was at fault but said the problem needed to be fixed.

"I expect federal Transport Minister Anthony Albanese and state Minister for Transport Terry Mulder to get their heads together and figure out how to cease that lease and decommission the old Mill Street site," he said.

A letter from Mr Albanese to Mr Forrest revealed that the State Government approved an Australian Rail Track Corporation proposal to grant Qube a short-term lease.

Member for Lowan Hugh Delahunty said Mr Mulder was investigating whether the State Government, as owner of the site, could terminate Qube Logistics' lease.

"I spoke to the minister about his rights and he felt that if anything was done, the State Government would have to give appropriate notification to Qube," he said.

"Now does appropriate notification mean one month or two months? I don't know.

"After my conversation with the minister, I understand his department is doing some work to be briefed on the issue."

Mr Delahunty said the State Government wanted the terminal shut.

"We didn't put a lot of money into the Dooen freight hub to have the Mill Street site run as it did before," he said.

"The minister is on the same page here the government's intention is to see that place decommissioned as soon as possible."

Mr Delahunty encouraged Wimmera Container Line and Qube to reach a commercial agreement allowing both companies to use the freight terminal at Dooen.

"Wimmera Container Line operates the terminal and in its lease it needs to allow other third parties access to the Dooen terminal at a reasonable commercial rate," he said.

"The argument is on between the two parties about what a reasonable rate is.

"I just hope the two operators can resolve their issues so we can move the freight to Dooen and decommission the old site."