It means travellers will not be able to book a place on trains between Edinburgh/Glasgow and Aberdeen/Inverness from 15 December.
The move will also affect Aberdeen-Inverness services.
The change, expected to last as long as six months, is understood to have been prompted by problems issuing reservations because three different types of trains are being used on the routes with different seat configurations.
That makes it difficult to match reservations with carriages because the type of train being used for a specific service might be changed at short notice.
ScotRail said the decision was “to avoid any mix-ups with reservations that would not be compatible between the different types of trains in service each day”.
Passengers will instead have to find a seat themselves as part of a new temporary “counted places” system.
This is because significant delays with the refurbishment of an acquired fleet of veteran “High Speed Trains” (HSTs) caused by US-owned refitter Wabtec in Doncaster.
It means some of them are still running in their “classic” state, along with some of the trains they will replace.
The Rail, Maritime and Transport union condemned the move.
Scotland regional organiser Michael Hogg said: “This policy will lead to conflict on our trains and a recipe for absolute chaos and disaster.”
"The [so-called] 'best railway Scotland has ever had' - yet ScotRail are proposing a system that has disaster written all over it."
Passenger watchdog Transport Focus urged ScotRail to reconsider the move and said a "free-for-all dash for seats" must be avoided.
Senior stakeholder manager Robert Samson said: "Although we understand the problems ScotRail are experiencing with the ongoing delay to introducing new trains on inter-city services, to suspend seat reservations on long-distance services in effect means that passengers have no guarantee of a seat over the busy festive period and beyond.
"Groups such as families will be disadvantaged, as will elderly passengers with luggage.
"A free-for-all dash for seats must not be the norm once the boarding process begins.
"ScotRail must have robust measures in place to ensure the proposed ‘counted place’ measure works, that vulnerable passengers are protected and the availability of advance purchase tickets is not reduced as a consequence of no seat reservations.
"We would urge ScotRail to reconsider this move and clearly demonstrate how this change will make life easier for passengers as is intended."
A memo to staff from ScotRail customer experience strategy manager Mark O’Mailley issued today stated: “From Sunday 15 December, the way we offer seat reservations will be changing.
“Customers using the InterCity services from Glasgow and Edinburgh to Aberdeen and Inverness are being advised they will not be able to reserve seats for a period of around six months.
“This means that when a customer purchases a ticket, they will receive a counted place booking for a specific service rather than an actual seat number as they would currently.
“This means that whilst the customer is ‘booked’ on a specific service, they will find their own seat when they board the train as they will not be allocated a specific one.”
“The reason we are changing to counted places on these routes for all ticket types is to try to make life easier for our customers and employees.
“While we gradually introduce more new trains into service and swap them out with older trains, we wanted to avoid any mix-ups with reservations that would not be compatible between the different types of trains in service each day.
“Seat reservations in their current format, will be suspended until the Classic HSTs and older trains have been removed from service and all the new refurbished HSTs are in place.
“We have plans in place to closely manage the capacity of our trains during this time.
“Our new HSTs are the longest that operate on these routes.
“Getting a seat during the transition won’t be a problem.
“Once the Classic HSTs and older trains are removed from service we will reintroduce consistent, reliable seat reservations on these routes.”
ScotRail said the Passenger Assist service, such as for wheelchairs, and bike reservations, would continue to operate normally.
A ScotRail spokesperson said: “We have been badly let down by our high-speed train suppliers Wabtec and Angel, which means we don’t have as many upgraded trains as we should have had at this point.
‘Because of their failure to deliver enough refurbished High Speed Trains on time, we have multiple different types of trains serving our intercity routes.
"This means we are unable to run the same type of train on the same service each day, which provides an inconsistent service for our customers.’
"As a result, for an interim period of time, we have replaced reservations.
"Importantly for our customers, we will continue to sell the cheapest advance tickets and manage quotas on our trains.
“The work we have carried out to monitor customer numbers on these key inter-city routes over the previous few months means we are confident this will provide customers with a more consistent level of service.”