Though the switch problems continued, regular service resumed about 1 p.m., but with some residual delays, the MTA said.
Riders reported a chaotic commute that started sometime before 10:30 a.m., according to social media and the transit authority's website.
Some southbound trains halted at Grand Central, while others were running, but with limited service, the MTA said.
Frustrated riders took to social media to rail against their difficult commutes.
"Train after train being pulled out of service, and hoards of people trying to pile up on the remaining 6 trains inching closer to their stops," user HMNbean posted on Reddit.
"Nearly 3hrs! New record to get to work! What's up @MTA? Sick rider, then switch problems and stuck in tunnel for 1hr," Amber Greene tweeted about 11 a.m.
"im stuck on four train , only couple stop away from where i get off but these delays is making 20 min ride to almost an hour," user Rjraymond posted on Reddit about noon.
An MTA spokeswoman could not say why the switch problems were occurring or when they would be resolved.
Riders were encouraged to take alternate routes.