Delays of up to 30 minutes were being reported on the New Haven Line just before 6 p.m. Tuesday.
Metro-North said the cause was a disabled Amtrak train near the East Norwalk station.
According to a tweet from Clever New Haven, the 4:50 p.m. train to New Haven was being moved backward from South Norwalk toward Rowayton, and only one track was open in East Norwalk.
Rail commuters also face problems on the Danbury Branch, after a tree fell across the tracks in Wilton. No word on delays or closures there had been announced, but stopped trains were visible near the fallen tree.
John Kovach and Susan Shultz contributed to this story