North Korea were supposed to stage the qualifier on Tuesday in the capital Pyongyang but five days before the game officials abruptly said the isolated country could not play host without giving a reason.
On Friday the Asian Football Confederation said the match was off and at the weekend FIFA said it "shall neither be played nor rescheduled", citing lack of space in the international football calendar, according to AFP.
"The matter and match outcome will be referred to the FIFA disciplinary committee," football's world governing body added.
North Korea could suffer a 3-0 forfeit as a result, which would send Japan into the third stage of qualifying for the World Cup in the United States, Canada and Mexico.
Japan beat North Korea 1-0 in Tokyo on Thursday to make it three wins from three in Asian qualifying Group B.
Coach Hajime Moriyasu, who took Japan to the last 16 of the Qatar World Cup after wins over Spain and Germany, had been eyeing the North Korea game as an opportunity to make improvements following an unconvincing display in the home leg.
"It's unfortunate that we lost the opportunity to correct areas of concern and potential areas for improvement that came to light," he said on Friday.
"We will aim to improve as a team based on what we have built so far."
Japan were dumped out of the Asian Cup quarter-finals 2-1 by Iran last month after entering the tournament as favourites.
