Work to repair three level crossings is due to take over a week, prolonging disruption to passengers.
Network Rail said no trains were currently running on the Marston Vale Line in Bedfordshire, between Stewartby and Bedford.
The issue lay with "automatic train detection systems" at level crossings in Marston, Green Lane in Stewartby and Kempston Hardwick.
Services are due to resume on Monday but with a "revised timetable".
London Northwestern Railway, which operates the service, said the problem started on 27 February.
Anyone travelling between Bedford and Bletchley needs to alight at Stewartby and get a replacement bus to Bedford.
From Monday, Kempston Hardwick level crossing is set to be closed to drivers.
James Dean, director for Network Rail's West Coast Mainline South route, apologised for the problems.
"Investigations are under way with the level crossing manufacturer and London Northwestern Railway to find out why the automatic system which lowers the crossing barriers is not working as it should", he said.
Lawrence Bowman, from London Northwestern Railway, said: "The safety of our passengers and staff is of paramount importance and we cannot allow trains to run until we receive the all-clear."
Passengers are being advised to check before they travel.