A tree toppled onto train tracks in East Williston Thursday and a mysterious smoke condition temporarily stopped a Port Jefferson-bound train, just two of the LIRR problems that added to headaches caused by Monday’s train derailment in Manhattan.

The Oyster Bay branch resumed service in both directions about an hour after a tree had fallen onto the Long Island Rail Road tracks about 5:15 p.m., said Shams Tarek, a spokesman for the Metropolitan Transportation Authority.

About 10 minutes after the tree fell, a “smoke condition” forced an eastbound train on the Port Jefferson branch to stop just east of Stony Brook, Tarek said.

“engine fire dead stop, waiting for rescue train to rescue us!” NewYorkCityNurse tweeted at 5:51 p.m., adding #SOS.

The train was cleared at 6:25 p.m. to move on, Tarek said, but the cause of the smoke was not clear.

Tarek said he doubted the engine was on fire, but did not know the source of the smoke, noting that it could have been caused by the train running over track debris.

“I don’t have any information there was a fire,” he said. “It likely was not. Sometimes, they’ll see smoke and think it was a fire.”

Just before 6 p.m., the LIRR began tweeting that several trains were up to 15 minutes late due to a broken crossing gate near Little Neck.

The disruptions come days after a NJ Transit train derailed Monday at Penn Station.

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Since then, the LIRR has canceled rush hour trains daily and reduced service because tracks have been off limits due to ongoing repairs.

Tarek said the MTA will monitor the overnight progress of repairs being undertaken by Amtrak, which owns the tracks there, before deciding whether to reduce service again Friday.