Prince Ali's countrymen were trailing 2-0 in Saitama to the Asian champions when Abdallah Salim was shown a controversial red card in the 27th minute for an elbow on Japan captain Makoto Hasebe.
Play continued before South Korean Kim Dong-jin sent off the Jordan forward. His team mates surrounded the referee and voiced their displeasure at the decision.
While Salim had his arm raised, replays showed his eyes were fixed on the ball as the two players tried to win a header near the halfway line.
Prince Ali, who is also president of the Jordanian Football Association, said: "I would like to express concerns over the refereeing we have witnessed thus far in the Asian qualifiers.
"It is certainly a highly important matter worth addressing with my colleagues on the AFC (African Football Confederation) executive committee. We are in need of a thorough assessment of our refereeing system.
"We should always strive to move forward in Asia and deliver what our players and fans deserve - fair play," added Prince Ali.
Despite the thrashing, which leaves Jordan with one point from two fourth-round matches and facing an uphill task to qualify for their first World Cup, Prince Ali said he had faith in coach Adnan Hamad.
"I would like to congratulate Japan for their well deserved win today. We are in a tough group and in a difficult match schedule but we accept the challenge," he added.
Jordan host Australia in their next World Cup qualifier in September needing to finish in the top two in the group, which also contains Iraq and Oman, to reach the finals in Brazil in 2014.