The group were rounded up after trying to cross the border "violently" and "illegally" on Sunday, the ministry said in a statement.
Video footage shows dozens of people - including women and children - running towards the fence that separates the two countries near the city of Tijuana.
They were repelled by tear gas used by US border officers.
Mexico's interior ministry said in a statement that a group of "nearly 500 migrants" had "tried to cross the border in a violent way".
Those identified as having taken part in these "violent events" would be deported immediately, it said.
The ministry added that, "far from helping their objectives", the migrants' actions had violated the legal migration framework and could have led to a "serious incident".
Tensions have been high in Tijuana since the arrival of thousands of migrants earlier this month.
The migrants are in Tijuana after travelling more than 4,000km (2,500 miles) from Central America.
They say they are fleeing persecution, poverty and violence in their home countries of Honduras, Guatemala and El Salvador.
However, they now face a long wait to see if their asylum applications will be accepted by the US, with President Donald Trump vowing to keep each migrant on the Mexican side of the border until courts have decided their case. This could take months.
Amid growing desperation on Sunday, the group of about 500 migrants were taking part in a peaceful protest for the right to seek political asylum in the US.
"We aren't criminals! We are hard workers," they chanted.
Mexico's Home Secretary, Alfonso Navarrete, said the group had asked for help to organise the demonstration, but were then reportedly encouraged by some of the movement's leaders to split into different groups so they could make a run for the border and try to cross into the US.
According to news agency AFP, a number managed to climb over the first fence. It was as they tried to cross a second, spike-topped wall that officials on the US side began throwing tear gas.
An AFP journalist saw the migrants - including mothers and children - trying to protect themselves from the gas, with some crying out that they only wanted to find a work and a better life in the US.
Associated Press journalist Chris Sherman said he had seen parents running away with choking toddlers.
Honduran migrant Ana Zuniga, 23, tried to cross with her three-year-old. She told AP: "We ran but when you run the smoke smothers you more."
Another Honduran, Joseph Garcia, told news agency Reuters he could not bear the wait any longer.
"I for one am desperate. My little girl is sick and I don't even have money for milk," he said. "I can't stand it anymore."
As a result of Sunday's action, the US closed the San Ysidro border crossing near Tijuana to vehicles and pedestrians for a time before re-opening it.
Mr Trump threatened to close the entire US-Mexico border earlier this week if it was felt the US was going to "lose control" of the situation.
He also said he had given troops at the border the go-ahead to use lethal force if needed.
Mr Trump has deployed about 5,800 troops to the border. He previously described the migrants as an "invasion".