Gunmen burst into the clinic where Jesus "El Kalimba" Martin was undergoing the procedure on Monday afternoon and executed him along with three other people, Puebla state prosecutors said.
Martin was wanted by the authorities for allegedly leading a fuel theft ring that illegally taps pipelines to steal gasoline and diesel -- a risky but lucrative business that has become Mexico's second-biggest organized crime problem after drug trafficking.
"He was trying to change his identity with a series of plastic surgery procedures to alter his face and remove his fingerprints so he couldn't be identified," prosecutors said in a statement.
"The medical personnel involved are also being investigated." Monday was a bloodbath in Puebla, where a total of 12 people were killed in what investigators say was a settling of scores between rival members of Martin's gang.
Five were murdered in the village of Tlaltenango on a farm where authorities found tubes, valves and pumps for illegal pipeline taps, as well as three stolen vehicles.
Three other victims appear to have been passersby caught in the crossfire, investigators said.
Prosecutors said the hits appeared to have been ordered by another crime boss known as "El Irving" who had the same rank as Martin within the gang.
Puebla is the epicenter of the booming fuel theft racket, which state oil company Pemex estimates has cost it $2.4 billion since 2010.
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