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Mexico's federal Civil Protection coordinator, Luis Felipe Puente, said 35,000 homes were damaged or destroyed and authorities raised the death toll across the country to 80.
Manuel struck the Pacific coast Sunday. Ingrid weakened from hurricane to tropical storm strength as it made landfall on the northeastern coast Monday.
Interior Minister Miguel Angel Osorio Chong said the weather systems affected 254 towns nationwide, forced 39,000 people to evacuate and caused 100 rivers to overflow. Several regions are still being battered by heavy rains and floods.
Officials said 40,000 Mexican and foreign tourists were marooned in Acapulco hotels after landslides blocked the two main highways out of the Pacific city, while dark, knee-high water covered the airport's terminal, leaving the the city of 680,000 people cut off.
Chong warned that it would take two to three days to reopen the two highways out of Acapulco, which lies in the hard-hit southwestern state of Guerrero.
The Mexican military, along with Aeromexico and Interjet airlines, began flying people out of Acapulco to Mexico City. Transport Minister Gerardo Ruiz Esparza said about 600 people had been flown out so far.
Aeromexico said it planned to fly 2,000 people out by Wednesday.
Meanwhile, Mexico may be facing another powerful weather system in the next few days.
The U.S. National Hurricane Center said an area of low pressure that is currently situated over Mexico's Yucatan peninsula has a 70 percent chance of becoming a tropical depression in the next 48 hours.
The system could spread heavy rains over portions of eastern Mexico and could cause life-threatening floods and mudslides, according to the NHC.