Electrical systems have been isolated while the cause of the smoke is investigated.
A fire and rescue spokespersons said: “There is currently no power to the loop meaning there may be some disruption to journeys.”
Train services on both the Chester and Ellesmere Port lines will run between Chester and Ellesmere Port and Birkenhead Central only, in both directions.
All services on the Hunts Cross line are currently suspended.
The same system will be in place on the West Kirby and New Brighton lines to Birkenhead North, between Southport and Sandhills, Ormskirk and Sandhills, and Headbolt Lane and Sandhills.