Japanese football chiefs have lodged a formal complaint with FIFA because they say their players were targeted by lasers during the 2-1 loss at Jordan.
Jordanian football bosses denied the claims.
"We filed a complaint with both FIFA and Asian Football Confederation about it. We are not sure if we will receive any answer from them," said a Japan Football Association (JFA) official.
JFA president Kuniya Daini told reporters late Wednesday he had been appalled by the actions of a minority of home fans at the game in Amman, when Jordan shocked the Blue Samurai.
"I hope such a thing will never happen again," he said.
"During the break at half time an announcement was made on the stadium speaker system warning fans not to use laser pointers."
Goalkeeper Eiji Kawashima and midfielder Yasuhito Endo had the lights -- which can cause eye damage -- directed at them.
Endo, who missed the penalty that would have given Japan the draw they needed to book a place at the World Cup finals, insisted the lasers had not distracted him, but said players had been coping with them throughout the game.
Jordan Football Association vice-president Salah Sabra said: "Personally, I am surprised at these accusations.
"We did not hear or notice anything about lasers. The Japanese players themselves did not complain during or after the match."
No one from FIFA was immediately available for comment.
Japan's shock loss scuppered their hopes of early qualification for the 2014 World Cup in Brazil.
Japan still lead Group B on 13 points, followed by Jordan on seven points, Australia and Oman on six points and Iraq on five points.
The Blue Samurai, who are aiming for a fifth straight berth to the World Cup finals, next play Australia at home on June 4.