The railroad said disabled trains are the culprits.
The certification puts Metro-North on a path to save $2 million annually by 2020 and further reduce its carbon footprint, MTA officials said
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The railroad said the cause is an earlier disabled train in the vicinity of Grand Central.
The New Haven Line is down to 30-minute delays, but the Harlem and Hudson lines are still operating limited service.
The railroad said a bridge strike had caused speed restrictions.
The closure is expected to last about two hours.