The late arrival of a new fleet on the main Edinburgh-Glasgow line will leave the operator short because the lease on four of its current trains expires in weeks.
ScotRail is so concerned at potential overcrowding that it will slash fares on another route between the cities by nearly half in an attempt to persuade commuters to switch.
The firm said it expected up to 12 trains a day to run with fewer carriages than normal from Monday, 26 February to 20 May.
It said those peak-hour trains, which normally operated with six carriages, would only have three or four.
That is the equivalent of at least fewer 1,500 seats a day, since each of the carriages being lost has 63 seats.
One ScotRail worker said: “When we lose those trains, we are in real trouble.”
ScotRail will try to offset the impact by dramatically cutting fares on a secondary Edinburgh-Glasgow route via Bathgate and Airdrie.
Peak-hour return tickets will be cut by nearly half to Â£13.
The offer starts on Monday, a week before the carriages start disappearing, in a bid to get regular travellers to make the switch.
However, journeys take around 20 minutes longer than the 50 or so minutes on the main line, and there is no catering trolley or tables.
The problem has been caused by ScotRail’s lease on four three-carriage class 170 diesel trains expiring at the end of the month.
They were due to be replaced by the first of a fleet of 70 new class 385 electric trains, but these have been delayed by a series of problems.
The first of the Japanese-designed Hitachi trains was due to have entered service last September.
Manufacturing hitches and delays to electrification of the line had put this back to late next month.
However, in a further setback revealed by Scotland on Sunday at the weekend, drivers threatened not to train on the them because of problems with seeing signals clearly from the cabs.
Scottish Conservatives transport spokesman Jamie Greene said: "It's bad enough for commuters that the new trains are delayed in entering service.
"We now find out rush hour trains are being taken out of service completely as the rolling stock leases are running out.
"It is unbelievably poor planning and reflective of a catalogue of management oversights on the Glasgow to Edinburgh improvement project."
A ScotRail spokesman said: “As we prepare for our brand new Hitachi class 385 trains, we are making some changes to our Edinburgh-Glasgow via Falkirk High service.
“This will result in a small number of services having a reduced number of seats.
“Customers should plan their journey in advance.
“We are sorry for any inconvenience this will cause customers.
“Customers travelling between Glasgow Queen Street and Edinburgh via Airdrie will be able to benefit from a reduced return fare of Â£13 - almost half the current price.”
The spokesman also stressed that some services on the main line were run by class 380 electric trains, which operated with seven carriages at peak hours.
He said they would not be affected.
The class 170 trains to be transferred by their rolling stock company owner to operators in England are understood to have already had their ScotRail livery removed.
A Transport Scotland spokesman said: “ScotRail are communicating with affected passengers to enable them to plan their journeys in advance, directing them towards trains which will still be operating at full capacity.
“We welcome the fare reduction on the Edinburgh-Glasgow route via Airdrie for those passengers who can opt for these alternative services.
“While we take the time, importantly, to listen to drivers’ concerns around windscreens, we are engaging closely with Abellio ScotRail as they look to introduce the c385 trains as quickly and smoothly as possible.
"This includes ensuring disruption to passengers is minimised during what we expect to be a short term impact on capacity on a small number of services."