The MTA and New Jersey Transit are both urging passengers not to use their Samsung Galaxy Note 7 mobile devices on its trains and buses.
The agencies on Tuesday told passengers they should turn them off before entering a station or boarding a vehicle because of concerns the device's battery can burst into flames.
Samsung has told owners to power them down and return them.
NJ Transit has not had any reported cases of the Note 7 catching fire. It's not clear if there have been any on New York city subways, buses or commuter rails, either.
Samsung, which recalled the phones from stores in 10 countries two weeks after the product launch, said it has confirmed at least 35 such cases.
NJ Transit in February restricted customers and employees from using, charging, storing or transporting hoverboards following similar fire safety concerns.
The Federal Aviation Administration has also issued a warning about using the Samsung Galaxy Note 7s on flights.