Morocco exited the tournament after finishing bottom of Group B, having lost against Iran and Portugal and drawn with Spain.
Lekjaa listed the key decisions that he felt were not given to Morocco as he called upon FIFA president Gianni Infantino to "remedy these injustices".
In a letter shared on the official FRMF Twitter account, Lekjaa said: "We wish to express our indignation regarding the injustice perpetrated against our national team, namely the string of serious refereeing mistakes which caused its elimination at the group stage of the 2018 World Cup.
"We believe without a shadow of doubt that the refereeing mistakes - especially those which occurred in the crucial games against Portugal and Spain - seriously hampered our team by denying it the chance to compete on an equal footing for qualification with the other teams in the group.
"The seriousness of the mistakes mentioned above is even more apparent when one considers the fact that in these two games (against Portugal and Spain), video technology was only used to benefit our rivals."
Lekjaa picked out three incidents from Morocco's 1-0 defeat to Portugal and five incidents from their 2-2 draw with Spain, including alleged fouls, penalty claims and incorrectly given corners that led to goals.
The letter continued: "We can only express our deepest concerns about the persistence of such injustices, and their negative impact on FIFA's image, as well as the football's future as a sport that is supposed to share and promote certain values, namely the equity and equality of all teams, and their respective chances of winning.
"Mister President, we know we can count on your 'elevated ethical code' and your belief in the rule of the law, so as to take measures which would impose the necessary adjustments so as to remedy these injustices and guarantee that each and every team is given the same chance of winning, above any other consideration."