A number of stations on the railway between Bletchley and Bedford could be closed under proposals for the East West Rail (EWR) line.
EWR said a number of stations may need to be consolidated or built to offer more services.
Trains only began running again on the Marston Vale line a year ago after a maintenance firm went bust.
A 10-week consultation on the plans, which could also see changes to stations in Bedford and more financial support for landowners, is under way.
EWR aims to create a railway connecting Oxford to Cambridge, via Milton Keynes and Bedford. The section between Oxford and Bletchley is due to open next year.
The project has been criticised by many local residents and politicians, but was given its backing by the government in the autumn Budget.
Transport Secretary Louise Haigh said: “More than £6bn in economic growth, 28,000 new jobs and tens of thousands of new homes are just some of the benefits East West Rail will deliver.
“Today marks a major milestone for the project as we encourage communities to have their say on this transformational line that will offer so much more than simply getting people from A to B.”
Under the current proposals, there would be up to four trains per hour.
EWR said it expected them to run from 06:00-00:00 Monday – Thursday, from 06:00 – 01:00 on Fridays and Saturdays, and between 07:00 and 23:00 on Sundays.
Under the proposals, stations at Bedford and Bletchley would be upgraded, although Bedford St John’s would be moved closer to the town’s hospital.
But it could mean changes for the other stations on the Marston Vale Line.
Option one involves retaining the existing 12 stations in their current locations, but option two would mean building new combined stations.
Which ones would be closed and where the new ones would be built is not clear.
But EWR stated that changes to this section would provide “a three-fold increase in services and reduce journey times”.
EWR said it would also be giving extra financial help to anyone whose land was affected via the proposals, in the form of “statutory blight provisions”.
It said this was in addition to the Need to Sell Property Scheme, for people who have seen the value of their homes depreciate because of the proposals.
A survey held earlier this year suggested 75% of people in Bedford supported the rail project.
Martin Yemm, who lives in Chawston and represented a campaign group on the matter, was one of the people surveyed.
Speaking in February, he told the BBC: “I find time and time again that you make a comment, that is then misconstrued completely and you get given an answer to something totally different.”
Proposals for the Cambridgeshire section of the route and options for the new station at Tempsford have also been announced.
The consultation on the updated proposals run for 10 weeks, from 14 November to 24 January.
You can take part online or attend one of the 16 drop-in events that are being held.