That order will go into effect on Wednesday at 8 p.m.
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That includes NJ Transit buses and private carrier buses, trains, light rail and Access Link vehicles.
"As we've undertaken our restart and recovery, and as more New Jerseyans are getting back to their jobs, we are seeing increases in ridership which are starting to approach the 50 percent stated maximum capacity for these vehicles," Murphy said.
"We want to ensure people can get to their jobs and the system is operating as efficiently as possible," he added.
Face coverings will be required for anyone using NJ Transit and private-carrier indoor stations. Face coverings are also required at outdoor stations where social distancing is not practical, Murphy said.
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The governor also reminded commuters that masks need to be worn over the mouth and nose.
"No chin guards," Murphy said.
Murphy also moved any special elections throughout the state to the November 3 general election.
The state reported 231 new positive COVID-19 test results on Monday, bringing the total since March 4 to 175,522.
Another 22 deaths were reported, bringing the total to 13,613. There are another 1,947 probable COVID-19 deaths, Murphy said.