"In general we have really good results but for sure ... many aspects should be improved," Massimo Busacca told a news conference.
VAR involves two video assistant referees who monitor the action on screens and draw the match referee's attention to officiating mistakes.
FIFA has already said it would like to use video assistant referees at the 2018 World Cup, and soccer's law-making body IFAB is expected to decide next March whether to allow them to become part of the game on a permanent basis.
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But their use has caused confusion at the Confederations Cup, especially during Sunday's match between Germany and Cameroon when on-field official Wilmar Roldan needed two reviews of an incident to send off the correct Cameroon player.
Cameroon coach Hugo Broos complained that he did not understand what was going on.
"I have to agree, it was too long... but in the end the right player was sent off," said Busacca.
There was also controversy when a video review denied Chile a legitimate-looking goal in their 2-0 win against Cameroon on June 18, and it was used again at the end of the same match to overturn a linesman's offside call and award Chile a goal
But the main criticisms are the time taken to make decisions and the referees' criteria in deciding when to use the system, with some close calls being made without consulting the VARs.
Busacca accepted that reviews could take the gloss off goal celebrations.
"It can reduce at some moments the enjoyment of football because you have a celebration and then suddenly a review and you have to change -- so people can have to live with this," he said.
In 12 group stage matches at the Confederations Cup, video review helped correct six "game-changing decisions," Busacca said.
Match officials ruled correctly on another 29 "major incidents" with the help of the technology, he added.
"It's important to mention today that clear mistakes were not missed," he said.
Busacca noted that if used correctly, the system could reduce many mistakes but not eliminate them completely. FIFA was keen on convincing member federations to use video review, he added.
Despite the controversy, FIFA President Gianni Infantino said this month he was extremely happy with its use at the tournament.
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