Officials visited North Korea's capital Pyongyang last week and gained an initial agreement that Japanese fans would be allowed to attend the Group B tie on June 8 JFA vice-president Junji Ogura said.
North Korean officials have asked the JFA for the number of their fans expected to make the trip.
The total is estimated at between 2000 and 5000 although the North Korean government has yet to announce how many visas will be granted.
One hundred Japanese journalists and 50 photographers will be permitted to cover the game on strict condition they report on soccer only.
Japanese fans are likely to arrive in Pyongyang on June 6 and leave on June 9.
Japan claimed a fortuitous 2-1 victory over North Korea in a tense opening game earlier this month. The JFA had allocated about 5000 tickets to Japan-based North Korean supporters.
The match was played amid tight security because of fears that bitter political divisions between the two countries might spill over.
The next matches in the final round of Asian qualifiers take place on March 25. The top two from each four-team group gain automatic qualification to next year's World Cup in Germany.