Scotrail said works between Croy and Falkirk High were expected to affect services until at least 11am.
The company said trains between Edinburgh and Glasgow via Falkirk High may be cancelled, delayed or diverted.
Company chiefs have apologised and urged affected passengers to claim redress under the Delay Repay Guarantee scheme.
On its website, Scotrail said: “To allow us to continue to run a regular service we’ve had to reduce the number of trains running between Queen Street and Edinburgh.
“Until we’re able to get back to a full schedule, we’re going to run services between Queen Street and Edinburgh every half hour.
“They’ll depart Queen Street on the hour and the half hour, and depart Edinburgh at quarter-past and quarter-to the hour.”
The company said that services running from Edinburgh to Queen Street would be diverted via Falkirk Grahamston. A shuttle bus will operate between Grahamston and Falkirk High.
Scotrail also urged passengers travelling directly between Queen Street and Edinburgh to consider alternative routes through Glasgow Central or Edinburgh to Queen Street Low Level via Bathgate.