The move was prompted by worries about whipping winds for trains and buses above ground and flooding concerns for trains running under rivers through one of 13 tunnels.
"Those tunnels may be flooded and we're worried a lot about that possibility," MTA chairman Jay Walder said.
WCBS 880's Rich Lamb reports: Residents Worried About Evacuating Without Mass Transit
Friday afternoon, the Long Island Rail Road released a list of the last trains that will operate on Saturday before the shutdown. You can find that list by clicking here.
"Please do not wait for the last train," Walder said. "There is simply not capacity for everyone to get on the last train. The sooner the people make decisions to be able the leave the better it will be for everyone."
Since it takes eight hours to shut the system down, equipment needs to be moved away from expected problem spots so maintenance can be done after the storm.
"Winds of this magnitude will be dropping trees all over parts of our railway so well be positioning equipment for that," Walder said.
Cuomo also said if wind speeds exceed 60 mph, area bridges will also be closed. Those include the George Washington Bridge, Tappan Zee Bridge, all bridges operated by the Triborough Bridge and Tunnel Authority as well as the Bear Mountain, Newburgh-Beacon, Mid-Hudson Kingston-Rhinecliff and Rip Van Winkle bridges.
Most riders that spoke with CBS 2's Sean Hennessey said they understood the need to shut down service.
"I've always felt that anything that they can do to protect the riders is the best thing. I really have no problem with that," said one man.
"If that's what the city needs to do, then safety first," said another man.
However, others on the LIRR were dreading getting into the city Saturday.
"I have to car pool with guys I work with," Brian Hall of Valley Stream told Hennessey. "It's just going to be a hassle."
New Jersey Gov. Chris Christie also announced Friday that NJ Transit will stop running at noon Saturday because of the storm. The Port Authority of New York and New Jersey is also bracing for Irene's arrival. The agency will suspend PATH service beginning at noon on Saturday.
"Service will resume as soon as conditions permit. The system is being closed to passengers so that trains and stations can be secured in advance of the storm, and protected against damage from high winds and water," the agency said in a statement.
The Port Authority also said it was bringing in extra staffing to deal with the situation at its airports. Heavy duty equipment is being brought in to deal with flooding as well as bottled water, diapers, cots, blankets, pillows and food for any passengers stranded at the airport during the storm.
When it comes to Port Authority-operated tunnels and bridges, the agency says depending on weather conditions, it may put restrictions on certain types of vehicles like tractor-trailers, motorcycles and car-pulled trailers.
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