The France international was caught in the head when he collided with Romelu Lukaku late on in Sunday's goalless draw.
Spurs boss Andre Villas-Boas defended his decision to let Lloris continue after a lengthy delay, claiming the 26-year-old had seemed "focused and determined to continue".
The club have since confirmed that Lloris underwent a "precautionary CT scan" which showed no issues and he returned home with the squad.
But FIFA's chief medical officer has also insisted that the Tottenham goalkeeper should have been substituted.
Professor Jiri Dvorak said FIFA's guidelines state that if there is any doubt about concussion then the player should be removed from the field of play.
Dvorak said there was a "99 per cent probability" that Lloris would have been concussed after being knocked out when his head made contact with Lukaku's knee. The Everton striker needed an ice-pack on his knee afterwards.
FIFA hosted a conference on concussion in sport a year ago, and earlier this year updated its guidelines, which are followed by the Football Association.
Dvorak said: "The player should have been substituted. The fact the other player needed ice on his knee means it's obvious the blow was extensive.
"It's a 99 per cent probability that losing consciousness in such an event will result in concussion."
Dvorak added that the player's view should not be taken into account in such situations.
He said: "When he has been knocked unconscious, the player himself may not see the reality.
"I do not know the details but I know that the Premier League doctors are extremely good and I can imagine that the doctor may have recommended he be replaced.
"We have a slogan: if there is any doubt, keep the player out."
Dvorak said any player suffering concussion needed to rest for at least a week - some advice states three weeks - and subjected to further tests.
Leading brain injury charity Headway said the club had displayed a "cavalier" attitude to the player's health.
Spokesman Luke Griggs said: "We are hugely concerned that a professional football club should take such an irresponsible and cavalier attitude to a player's health.
"When a player - or any individual - suffers a blow to the head that is severe enough for them to lose consciousness, it is vital they urgently seek appropriate medical attention.
"A physio or doctor treating a player on the pitch simply cannot accurately gauge the severity of the damage caused to the player's brain in such a setting as there may be delayed presentation of symptoms.
"By continuing to play, the player may have caused greater damage to his brain. He should have been removed from the game immediately and taken to hospital for thorough tests and observation.
"Sports science has evolved significantly over the past decade and yet we're still faced with the antiquated concept that a player should be brave and try to continue at all costs. Mr Villas-Boas' comment that his player's determination to play on was proof of his "great character and personality" is simply wrong and dangerous.
"You are not a hero if you play on after suffering a concussion; all you are doing is risking your health. Football has to react to this and bring in stricter measures to ensure no similar risks are taken in the future."
FIFA's concussion guidelines, also agreed with the international rugby union, ice hockey and equestrian federations, state: "With every impact to the head, it is important that you always think of concussion and watch out for it. If you feel a little out of sorts, but think you can still play, that may not be a good idea. The safest is: "when in doubt, keep out"."
Problems with concussion are not commonplace in football, but rugby players from both codes have to deal with significant blows to the head on a regular basis.
The problem became so worrying for Dr Barry O'Driscoll, uncle of Ireland player Brian O'Driscoll, that he resigned from his role as medical advisor to the International Rugby Board in protest at the decision to trial a new protocol for dealing with head injuries.
The Rugby Football Union is so concerned about concussion that it is holding a conference at Twickenham this week with players' unions on the matter.
Villas-Boas admitted after the final whistle that his goalkeeper had not remembered the moment of impact.
"The medical department was giving me signs that the player couldn't carry on, because he couldn't remember where he was," Villas-Boas, speaking after the stalemate, said.
"But he was quite focused and determined to continue, so when you see this kind of assertiveness it means he is able to carry on, and that is why it was my call to delay the substitution.
"You have to make a decision in situations like this but from my knowledge of Hugo he seemed okay to continue."
Villas-Boas added: "It was a dreadful situation. You can imagine the impact of a knee going against a goalkeeper's head.
"It happened unfortunately to Petr (Cech) so it is good that the players immediately went to him and it is very fortunate that it was nothing serious."
I don't understand why he was not taken off. For the sake of someones health and with only 15-20 mins of the game left, Friedal should have clearly gone on. With the criticism (deservedly) being flung at AVB, I personally think the referee should be held equally, if not more accountable for continuing the game like that...... I notice FIFA aren't criticising him.- blokeinkent