The track condition was reported at about noon. The railroad said the track would take about 20 minutes to repair. It was not immediately clear if the break was weather-related or if additional repairs were necessary.
The line is single-track in that area.
The break delayed the 11:42 a.m. train from Greenport, due to arrive in Ronkonkoma at 1:06 p.m.
Earlier, service on the Ronkonkoma branch had been suspended for about 2 1/2 hours through Deer Park because of a power outage, the railroad said.
Service was suspended in both directions just after 5 a.m. and wasn't restored until about 7:30 a.m., officials said.