Friday morning’s LIRR commute should be back to normal, an Amtrak official said, after a second power outage Thursday bedeviled commuters.

Amtrak spokesman Mike Tolbert said late Thursday that workers “are still working to address the power issue, but anticipate normal operations for the morning rush” on Friday.

Amtrak, which owns and runs Pennsylvania Station, said on Thursday that the power system problem knocked out 12 of the station’s 21 tracks as well as one of the four East River tunnels.

The LIRR, which must share the tracks with the national railroad and New Jersey Transit, first warned an Amtrak power problem would cause delays at about 5 p.m.

The evening problems — cancellations and 10- to 15-minute delays systemwide — follow a snarled morning, also blamed on Amtrak.

LIRR’s Thursday morning commuters were delayed by nearly half an hour after an Amtrak third rail power problem caused a train to become disabled outside an East River tunnel, just before it was due to arrive in Penn Station.

advertisement | advertise on newsday

But the evening outage was a different problem.

An Amtrak spokesman said the latest issue “appears to be a separate issue affecting tracks 1 through 12.”

“Amtrak crews are working to address a power system issue affecting several station tracks,” spokesman Mike Tolbert said in a statement at about 5:30 p.m.

Power was also out in one of the East River tunnels, reducing track capacity during the evening rush, the LIRR said.

The evening problems erupted less than two hours after Amtrak said the morning power problem had been fixed, and the LIRR advised its passengers trains were running on or close to schedule.

On Thursday morning, about 500 people were stuck for nearly two hours on the 5:09 a.m. from Port Washington after it became disabled just outside the tunnel, LIRR spokesman Aaron Donovan said.

The delays were cut as the morning wore on, and by noon they averaged only 10 minutes, with most branches reporting that their schedules had returned to normal, according to Donovan.

Earlier riders on all lines had been warned to expect delays and cancellations heading into Penn as a result of the track condition.

advertisement | advertise on newsday

The problem was reported about 6:30 a.m., Donovan said. Until about 9:45 a.m., average delays were 20 to 25 minutes, he said.

Just before 12:30 p.m. Thursday, Amtrak spokesman Mike Tolbert said the cause of the outage was under investigation.

Donovan said some westbound trains had been diverted to Hunters Point Avenue in Queens and Atlantic Terminal in Brooklyn. Donovan said five trains were canceled and five were canceled en route before their final destination.

Donovan said the cancellations, reroutings and delays were due to reduced track capacity, with one of Amtrak’s four East River tunnels out of service as a result of the third rail incident. The stretch of third rail track involved is owned and maintained by Amtrak, Donovan added.

The disabled Port Washington train stopped just two minutes before it was due in Penn Station at 5:52 a.m. when it encountered “a problem” just outside an East River tunnel, Donovan said. He said an LIRR train connected to the disabled train at 7:40 a.m. and transported passengers to Hunters Point Avenue, where they were cross-honored by New York City Transit on the No. 7 train.

advertisement | advertise on newsday

The passengers arrived at Hunters Point Avenue at 8 a.m. and were met by MTA Police and New York City fire personnel who offered them assistance, including directions on how to get where they needed to go, Donovan said. Customers were provided with water by members of the train crew and there were no self-evacuation of customers or injuries reported.

New York City Transit cross-honored LIRR tickets at Jamaica, Atlantic Terminal, Kew Gardens, Forest Hills, Hunters Point Avenue and Woodside.

Earlier Thursday, the LIRR said riders on the Montauk line should expect canceled trains and delays averaging one hour after a fire caused signal damage near the Mastic-Shirley train station, the railroad said.

The fire was reported about 10 p.m. on LIRR property, Gamerman said.

Firefighters brought the blaze under control shortly before midnight, Suffolk County officials said.

William Floyd Parkway was shut down in both directions as firefighters responded, but it was reopened before the morning rush hour, police said.

With Lisa Irizarry and Alison Fox