"At this time (are) 97 deaths from these two natural phenomena, " reported Xinhua citing Luis Felipe Puente, National Coordinator of Civil Protection.
There were also 58 people missing after a massive landslide smashed a small village in the country's southern mountains, he said.
Local authorities were taking efforts to determine whether the missing were still alive, although Guerrero State Govenor Angel Aguirre said "it's very likely these 58 missing people lost their lives".
So far, 344 people have been rescued from the village of La Pintada with federal helicopters, some of whom injured and one in serious condition, said Mexican Interior Minister Miguel Angel Osorio Chong, adding that another 46 will be flown out of the area Thursday.
Heavy rains pouring over the village could trigger more landslides and increase the risk for rescue workers to evacuate the last residents from the village, the minister said.
Storm Manuel, with maximum sustained winds of 120 km per hour entered the Sinaloa state, the northwestern coast of the country, National Weather Service said.
Sinaloa state civil protection authorities said some areas were flooding and that over 200 people were evacuated from small fishing villages on the coast.