The Women's World Cup is not "an experiment" for new laws and criticism of the use of video assistant referees has surprised Fifa, says its head of referees Pierluigi Collina.
England manager Phil Neville said this week Fifa has "major decisions to make" regarding the use of VAR.
World football's governing body says the same rules have been implemented across all competitions from 1 June.
"The only issue, apparently, concerns penalty kicks," said Collina.
"And honestly we have been a bit surprised."
The Italian was referring to a rule regarding encroachment from goalkeepers when saving penalty kicks - with the spot kicks then being retaken and the player being cautioned.
Scotland goalkeeper Lee Alexander saved a late penalty in her side's 3-3 draw with Argentina but a retake was ordered after the video assistant referee ruled she had moved of her line.
The retake was scored and Alexander became one of three players to have received a yellow card for encroachment during the tournament.
France also benefitted from a similar situation in a group game when a penalty against Nigeria hit a post.
Nigeria keeper Chiamaka Nnadozie was ruled to have moved off her line early by VAR and Wendie Renard scored the winner from the second spot-kick.
Italy also scored their first in a 5-0 win over Jamaica with a retaken penalty after goalkeeper Sydney Schneider was punished for moving off her line in saving the initial spot-kick.
The decisions were correct, according to the new laws which came into effect on 1 June and were outlined by the International Football Association Board (Ifab), though Fifa has since said goalkeepers will not be booked if they break the rule during a shootout.
Collina said world football's law-making body had changed the rule to help goalkeepers by allowing them to just have one foot on or level with the line rather than two.
"We acknowledged that saving a penalty by keeping two feet on the goalline until the taker kicks the ball makes the goalkeeper's job almost impossible," he added.
"If something is written in the laws of the game it must be respected.
"It is not a matter of a small encroachment or big encroachment, it is a matter of encroachment, and this is what we can do by using technology."
England boss Neville said Fifa had to look at the use of VAR after controversy around decisions dominated the group stage, while Manchester United Women manager Casey Stoney said it is "ruining the game".
Collina refuted claims teams at the tournament in France were being used as "guinea pigs", saying new rules are always implemented from 1 June and that has previously been the case at men's World Cups.
"Were the World Cup in '98 and Euro 2016 considered as guinea pigs because a new law was implemented?" he said.
"New laws are implemented on 1 June, tournaments played in summer are played with new laws. This is something that has been going on for many years."
Speaking at a media briefing, he added: "We didn't consider the Women's World Cup, which is our flagship tournament in 2019 as a World Cup, we cannot consider this competition as an experiment."
The Premier League has said it will use VAR for the first time for the 2019-20 season but will not use it to rule on goalkeepers moving off their line to save a penalty.
Professional Game Match Officials Limited (PGMOL) will leave such decisions to on-field officials, though it could review the situation during the season.
However, Collina said he was unaware of this and "the rules of the game must be enforced in every country and competition".
"You cannot decide how to enforce the rules of the game," he told BBC Sport. "If you don't like something you need to respect the laws of the game, that is what we are enforcing here in France."