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People smashed car windows and threw objects towards cars which were operated by Uber-registered drivers.
At least eight vehicles were damaged during the incident, which took police around half an hour to control.
There have been widespread protests across Mexico this week as traditional taxi drivers raise their fears of Uber’s effect on their livelihoods.
The drivers’ union – Organised Taxi Drivers of Mexico City – says that while its drivers were not involved in the latest attack, they are nonetheless angered by Uber’s encroachment on their industry.
"These transnational applications are infiltrating different countries as an economic parasite, endangering the livelihood of thousands of taxi drivers and their families and devouring the market for the legally established service," union official Ignacio Rodriguez told the Associated Press.
LaJornada obtained footage of the attacks which took place close to the city’s airport on Tuesday.
Rocio Paniagua from Uber Mexico said: “What happened yesterday is a very serious incident which we condemn and is unacceptable in Mexico and in any other city in the world.
"Violence is unacceptable, we invite everyone to have a dialogue and we’re open to working with authorities and taxi associations to benefit citizens.”
In July, the AP reported new regulations governing Uber and other smartphone ride-share apps – allowing their operation despite the concerns of licensed cabbies.
Those operating cars for Uber have to submit to yearly inspections, and they can’t take cash for their services.
Mexico City is the largest metropolitan area to introduce clear regulations.
Protests by traditional cab drivers against the introduction of Uber have taken place in cities across the globe, including London.