Several tracks at Penn Station are now closed for repairs, and the number of trains coming into Manhattan has been drastically reduced.
The eight-week infrastructure renovation project is expected to cause major disruptions for hundreds of thousands of commuters, but most were grateful that the first test went off without a hitch.
"We have to remain vigilant and make sure trains stay on time," said Joe Lhota, MTA Chairman of the successful first day.
"We like to think it's quiet because a lot of people did their homework," New Jersey Transit spokesman Charles Ingoglia said while standing outside the Hoboken train and ferry stations.
Twice as many commuters used Atlantic Terminal in Downtown Brooklyn between 6 a.m. and 6:30 a.m., an early indication that Long Island Rail Road riders are taking the MTA's advice and transferring to service away from Penn Station.
More commuters arriving at the Hoboken Terminal seemed to be using the ferry to get across the Hudson River than PATH, and Hoboken police said they saw less commuters at the Hoboken Terminal overall.
New Jersey Transit said they had more room for people to take ferries, encouraging commuters to try that route.
The three railroads that use Penn Station - Amtrak, the LIRR and New Jersey Transit - are reducing service at peak periods during the repairs, which are expected to last until the end of August.
LIRR commuters can expect to see a 20 percent reduction of service, while on New Jersey Transit, Midtown Direct trains will not go into Manhattan.
But officials say there are many alternatives.
The LIRR will allow commuters to board larger trains, ferry and bus service, and a combination of rail and subway. New Jersey Transit is offering a similar plan, while Amtrak has also modified its daily train schedules.
"We thought long and hard about how to make this, what's going on with Amtrak, try to make this as easy as possible for them, to provide an array of options so that everyone can get to work on time and that everybody will be able to get home in the evening," Lhota said.
He added that not as many people used the buses or ferries as they expected, but noted that this is just the first day and the agency will have to watch and see and adjust where necessary.
Governor Cuomo announced that ahead of the repair work, all non-emergency construction is suspended from 5 a.m. until 10 p.m. and all lanes are open on major roadways in the New York City area, in an effort to assist with LIRR bus service.
On Monday, Amtrak's infrastructure renewal began in the spaghetti junction of tracks and switches in what's known as "A-Interlocking."
Penn Station handles more than 650,000 commuter rail and Amtrak passengers each day. The passengers come through seven tunnels - the rail lines then switch to 21 platforms.
The long-overdue repair work takes out three to five tracks at a time in the A-Interlocking section, a critical switching area used by Amtrak, New Jersey Transit and the LIRR.
"We will go down to three tracks during the peak periods to more readily accommodate service at the peak periods," Amtrak COO Scot Naparstek said.
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(The Associated Press contributed to this report.)