The weekend announcement from Japan's transport ministry follows an earlier warning that asked airlines to urge passengers not to turn on or charge the smartphones on aircraft.
But aviation authorities went a step further on October 15, ordering airlines to ban the devices completely, a transport ministry official said.
The South Korean electronics giant has recalled all Note 7 phones, including replacements, following reports of exploding batteries and fires, which have led to numerous injuries. Samsung has also stopped producing the flagship handset.
Japan's move came after US transport authorities on October 15 issued an emergency order banning the phones and saying anyone attempting to travel with the recalled handsets may face fines and have the devices confiscated.
It was not immediately clear what sort of penalties passengers on All Nippon Airways and Japan Airlines (JAL) – the country's biggest carriers - could face if they were found with the phone.
JAL spokesman Takuya Shimoguchi said customers could choose to board planes without their Note 7 phone or the airline would confiscate it. But "there have been no clear instructions on punitive measures, We'll act on a case-by-case basis."
Korean Air follows government guidelines requiring Note 7s to be turned off in-flight and only transported in carry-on luggage. But it operates a total ban on flights to-and-from the US, Canada and Hong Kong.
South Korea's Asiana has banned Note 7s from all flights starting October 17. Australian and New Zealand airlines have also banned the phone from all planes.
Almost all mainland Chinese airlines have also banned it, while at the weekend Hong Kong's international airport prohibited passengers from carrying the device on any incoming or outgoing flights, either in checked or carry-on baggage.
The southern Chinese city's flagship carrier Cathay Pacific and its low-cost offshoot Dragonair had also said passengers were no longer allowed to carry the devices on any of their flights.
They were joined by Hong Kong Airlines and Hong Kong Express - two of the city's budget carriers.
Singapore Airlines and Taiwan's two biggest airlines China Airlines and EVA Air have also banned the smartphones.