Runner-up Vivian Noronha of Brazil will receive the crown.
The company statement did not specify what pageant rules were broken by Zuniga, who was detained in western Mexico on Dec. 22 along with seven men, some of them suspected drug traffickers. Authorities found a large stash of weapons, ammunition and $53,300 with them inside a vehicle.
Zuniga told police the group planned to travel to Bolivia and Colombia to go shopping.
Zuniga still holds the Miss Sinaloa title from a Mexican state beauty contest in July. And she placed third in the Miss Mexico contest, whose winner competes for the Miss Universe title. As third-runner up, she was expected to represent Mexico in the 2009 Miss International contest.
Miss Mexico pageant organizers say they are awaiting the results of the investigation before deciding what to do.
But doubts are already beginning to arise about Zuniga's string of pageant victories, after a Sinaloa state official told local media that she may not have gone through the proper auditions for the Miss Sinaloa contest.
"Everything indicates she won her crown through the intervention of her boyfriend, a drug lord," wrote columnist Carlos Puig in the Mexican newspaper Milenio.
While there is no hard evidence that the slender, striking Zuniga improperly won any of her titles, Mexican drug traffickers are know to take innocuous contests seriously.
In November, 17 people - most suspected traffickers - were killed in an argument over bets on a horse race in an area near the Mexico-Guatemala border.