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Domestic passenger numbers fell 2% last month, while international passengers were down 6.7%, the company said in a release.
Los Cabos airport was closed for more than a week due to the hurricane and reported a 41% drop in passenger numbers for the month.
The speed of the airport's recuperation will determine the effects of the hurricane on Q4 results, said the company.
Fellow airport operator Asur reported a 10.5% year-on-year increase in total passenger traffic in September.
According to a company release, 1.47mn passengers passed through Asur's nine airports last month, up from 1.33mn passengers in September 2013.
Domestic passengers increased 12.9%, while international ones rose 7.8%. Cozumel airport in Quintana Roo state saw the highest growth, with 23.7% more passengers.
Airport operator OMA reported 10% year-on-year passenger traffic growth in September.
Domestic traffic grew 9.6%, while international traffic increased 13.1%, the operator said in a release.