The Long Island Rail Road was thrown into chaos during the morning commute Wednesday after a train struck debris that had fallen in an East River tunnel, officials said.

Eight of 11 LIRR lines were delayed or cancelled as passengers in the train had to be evacuated from the tunnel, one of four under the river that are operated by Amtrak and used by several commuter lines.

The havoc included trains diverted to Grand Central Madison and others forced to end service at Jamaica, where passengers had to transfer to subway lines or other trains to reach Manhattan.

“All I can tell you right now is we hit a piece of metal,” LIRR president Rob Free said Wednesday.

Just before noon the Babylon Branch, City Terminal Zone and the Port Washington Branch were still delayed because service into Penn Station is still restricted as crews inspect the tunnel and work to resolve the issue.

Free said they wouldn’t know until later in the day if trains would be back to normal schedules in time for the evening commute.

The problem started around 4 a.m., when a New Jersey Transit train first got stuck in the tunnel. A spokesperson for NJT did not respond to The Post’s request for comment. 

Around 6 a.m. the LIRR train also got stuck in the same tunnel, Amtrak confirmed.

“We are determining where this debris came from and the cause of the issue with the first train,” read a statement from Amtrak.

There are four train tunnels under the East River. Amtrak is conducting repairs in Line 2, but the trains got stuck in Line 4.

Riders complained of packed platforms, longer travel times and confusion about last‑minute changes to their usual routes, according to a report from CBS. 

The disruption underscores how little margin there is in the East River tunnels as one tube is out of service for repairs leaving only three tunnels to be shared by Amtrak, NJ Transit and the LIRR.