Selling alcohol to people under 18 is illegal in Mexico and nightclubs are allowed to operate only within certain time limits.
However, those laws are largely ignored by bar and nightclub owners.
Around 1,000 people were inside the disco to celebrate the end of the school year.
Cases of beer were said to be blocking the emergency exit.
At a news conference later on Friday, Ortega said about 500 young people - more than the club's capacity - were there to celebrate the end of the school year and many more were waiting in line to get into the nightclub.
"Unfortunately, the person in charge of the nightclub took the microphone and announced a police operation was underway," Ortega said.
He also said that people panicked and rushed to get out, causing a stampede.