The savings emerged yesterday as a six-month consultation on the £1 billion Edinburgh Glasgow Improvement Programme (EGIP) was formally launched.
Sources at Network Rail, which is delivering the programme on behalf of the Scottish Government, said its true costs had been reduced by between £100m and £200m compared to its official budget as more efficient working practices had been identified.
"The project budget was £1bn a year ago but we are now expecting it to come in at between £800m and £900m," a senior official said.
As well as speeding up journeys between Scotland's two biggest cities, the project, due for completion in five years, will see more than 200 miles of track electrified on eight routes, improving services to Stirling, Alloa and Dunblane, and increase the number of trains running between Edinburgh and Fife.
A number of stations will undergo significant upgrades, including Edinburgh Waverley, Haymarket and Glasgow Queen Street, which may require an additional platform in order to handle the increase in train services, while a new interchange is planned to connect with trams near Edinburgh airport.
Martin Murray, Network Rail's project manager for EGIP, said more efficient working practices developed over the last year have helped cut costs and said additional savings may yet be identified before it is completed in 2016.
"The costs are coming down as we've been looking at different methods of construction," he said.
Many of the savings identified on EGIP are down to advances in techniques for erecting overhead cabling and improvements in erecting bridges, which now typically take a weekend to put up rather than a week. The establishment of a new partnership working group with suppliers is also expected to contribute to savings.
A Transport Scotland spokeswoman said: "We consistently look to secure best value for money on projects, and this £1bn scheme is no exception.
A spokesman for Network Rail added: "While the current cost is a realistic assessment for the works, we are committed to getting the best value for money we can and we will be seeking to identify significant savings across the programme as it is delivered."