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Four bodies were found in the municipality of Los Cabos, the other two near the state capital of La Paz. The bodies were found suspended from three bridges located near the two main international airports and the highways leading to the popular beach resort of Cabo San Lucas.
Authorities have not released the identities of the deceased nor said who they believe to be responsible for the deaths.
The six cases are being investigated as homicides, the attorney general's office said.
Violence in the Baja California Sur region has increased in the past three years, due to an ongoing territorial dispute between the Sinaloa and Jalisco New Generation drug cartels.
Mexico's notoriously ruthless drug gangs have regularly hanged victims from bridges and highway overpasses in places like Mexico City, but it is unusual for bodies to be seen near tourist areas.
In August, the US State Department issued an updated travel warning, cautioning tourists that the state experienced an "increase in homicide rates" compared to the same period in 2016.
Rodrigo Esponda, managing director of the Los Cabos Tourism Board, told HLN that the region is a "safe and secure destination, as it always has been."
The area, which sees 2 million international visitors per year, will get 200 new police officers early next year.
Los Cabos is also making progress on expanding its surveillance system, Esponda told HLN, adding new cameras and wiring existing hotel security cameras into a centralized crime reporting system. A military base is being built, too, he said.
CNN's Steve Almasy contributed to this report.