ARU chairman Dilip Kumar and JRFU president Yoshiro Mori have pledged their support in helping the International Rugby Board achieve its strategic goals, particularly in the Asia-Pacific region.
The two countries believe the agreement can help to improve the competitiveness within Tier One rugby-playing countries such as Australia, New Zealand and South Africa, as well as developing high-performance programmes in Tier Two countries, such as Japan, Fiji, Samoa and Tonga.
Kumar believes the ARU has a responsibility to the development of the game in these countries.
"Ultimately, we would all like to see an increasing number of teams which have a realistic chance of making the semi-finals of the Rugby World Cup," he said.
"We already maintain strong ties with Japan through Eddie Jones and Glen Ella, who have offered assistance to the national team in the past.
"Many Australians continue to play club rugby in Japan, Australia hosts frequent tours by school, university and club sides and there is an ongoing exchange at referee level."
Mori said Japan believes Australia can assist in the improvement in the quality of Japanese rugby to the point where they could be in a position to challenge for a quarter-final place at future Rugby World Cup tournaments.
"The JRFU values its relationship with Australia. Through this accord, we will access greater technical advice and sports science advice for our national team, explore new competition options and establish coach, player and referee exchanges," Mori added.
"Both our Unions are very enthusiastic about the outcomes that can be achieved through the accord."
Japan were one of the best-supported teams during the 2003 Rugby World Cup in Australia with local fans flocking to their matches in Townsville and Gosford.