The Aberdeenshire railway line where three people were killed in a train crash won’t open until October.
And the Glasgow to Edinburgh mainline will also remain closed for “a number of weeks” after a landslip.
Transport secretary Michael Matheson said investigators are still examining the cause of the Stonehaven rail crash last month, but are finding it “very difficult” to access the site.
Train driver Brett McCullough, 45, conductor Donald Dinnie, 58, and passenger Christopher Stuchbury, 62, died when the 6.38am Aberdeen to Glasgow Queen Street train crashed into a landslide across the tracks near Stonehaven on August 12 following heavy rain.
Matheson, who was updating MSPs on Holyrood’s rural economy and connectivity committee, said the site was under the control of Police Scotland, who are investigating the crash along with British Transport Police.
He said: “The challenge which they have experienced is access to the site. It is a very difficult area for the engineers and for the investigators to access.
“At the present moment significant work is being undertaken in order to provide an access road into the site, which is now at a very advanced stage.
“Once that has been complete and the investigations has been complete, Network Rail and engineers will be in a position where they can start the recovery phase of the process.
“My expectation is that the line will remain closed for passenger use into October, given the scale of the challenge they face moving into the recovery phase once the investigation has been completed.”
The transport secretary also said travellers between Glasgow and Edinburgh would continue to face disruption for a “number of weeks” after a canal burst during a storm resulted in damage to the track between Linlithgow and Polmont.
Matheson told the committee: “The Union Canal, which breached and swept away almost a kilometre of the rail bed on the Glasgow Edinburgh line, has been plugged. There is now extensive recovery work being undertaken.
“I expect it will be a number of weeks before that repair work is complete.
“It has not only swept away a kilometre of the actual rail bed, it has also swept away the electrical infrastructure, the overhead lines, the foundations etc have all been swept away. It is very extensive, the level of damage that has been caused.”