The Spaniard thinks there is currently too much pressure on coaches to send someone back on who has just been knocked out if they have already used their maximum three replacements.
And the Toffees boss also leapt to the defence of Romelu Lukaku after Tottenham's Andre Villas-Boas said questions needed to be asked of the Belgian striker's role in the collision which saw goalkeeper Hugo Lloris lose consciousness during Sunday's goalless draw at Goodison Park before he continued in the game.
"It would be very unfair to be a manager in a position where you have to take a player off just to avoid any sort of risk without having that medical knowledge," said Martinez.
"My view is that I don't think it should be a manager's decision whether you take a player off or not.
"If there is a strong view from the medical side that when a player gets concussed he should come off, I think we should look into it and make it a rule.
"If it comes as a rule with an understanding for everyone that if that happens the player should come off and it shouldn't count as a substitution, that would be a lot easier.
"Because if you are put in a position where a player has to come off when three substitutions have been made it is a real shame, as it is going to affect the competition.
"You wouldn't want to see a team down to 10 men but the last thing you want is to put the health of any player at risk.
"It is a serious issue which needs to be spoken about and the right decision found from the top."
Villas-Boas claimed Lukaku could have avoided his knee connecting with Lloris' head and asked why more questions had not been directed at the striker and why he had not apologised.
But Martinez responded, suggesting there should have been a similar conversation the other way regarding Roberto Soldado's apparent elbow on Phil Jagielka.
"The good thing is you can watch the replay and see the video evidence," said the Spaniard.
"All Romelu is doing is carrying on his run, he cannot disappear. It is unfortunate.
"I don't think Andre Villas-Boas mentioned there was any intent or any wrongdoing from Romelu, he only mentioned he expected a bit of an apology.
"Obviously we are waiting for Roberto Soldado to apologise to Phil Jagielka and so we can use the same phone call, so we don't have to spend on two phone calls."
Asked whether he thought there should have been retrospective action taken against the Spain international, Martinez said: "That is not for me to comment. I don't think it would give anything to Everton.
"That is down to the authorities to decide whether they want to implement it.
"I am more about the referee making decisions in the game and whatever happens in the game is where it matters.
"I'm not too keen about retrospective punishment unless it (the action) goes against the values of the competition.
"I don't think they (officials) saw it, obviously, otherwise they would've acted accordingly.
"Nowadays you have action replays and you can see everything that happens but for the referee it is very difficult."