The commute home using Muni’s railway system is going to be a slow one.

Delays in the downtown subway tunnel began around 6 p.m. Wednesday near Church Station when a train control, which affects the entire automated system, malfunctioned, Muni spokesman Paul Rose said.

As a result, trains were halted for a period of time. Trains are now moving slowly through the area, but riders can expect significant delays for the next hour, Rose said.

Crews are working to resolve the problem, but there is no estimated time it will be fixed. Shuttles are running on Market Street and the F-Market line is operating, Rose said.

akoskey@sfexaminer.com