The Long Island Rail Road said it was operating on or close to schedule during Thursday’s morning rush hour after an issue in an East River tunnel had created delays, cancellations and some diverted trains.

At about 7 a.m. the rail service said in an email alert that the tunnel issue could cause customers to wait; about an hour later it said most schedules were back to normal or close.

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Some trains were diverted to either the Atlantic Terminal or the Hunterspoint Avenue stations because of the issue.

During the period, NYC Transit also cross-honored LIRR fares via the 2/3 subway at Atlantic Terminal, the 7 subway at Hunterspoint Avenue and the E train at Jamaica station, the LIRR said.