Hurricane Jova, which has now been downgraded from a category three hurricane to a category one tropical storm, claimed its first victims in Jalisco on Wednesday.
Two people died after being caught in a landslide in the municipality of Cihuatlan, one of the areas worst affected by the storm.
Secretary General Fernando Guzman Perez Pelaez confirmed the victims were five-year old Yolanda Marisol Rebolledo, and her 21-year old mother, Norma Irene Rebolledo.
Three others were injured in La Huerta on Tuesday night, while two children were hurt in the small coastal town of Tomatlan when the roof of their home collapsed.
There have been no reports of injuries in the popular resort of Puerto Vallarta, which was badly flooded when Hurricane Kenna hit the area in 2002.
The state government confirmed Wednesday morning that at least 500 people have been evacuated from their homes and around 160 are now in temporary shelters.
Elements of the army are coordinating with state and municipal authorities to gain access to villages where thousands of people are currently isolated.
Virtually cut off due to floods and constant landslides, the municipalities of Cihuatlan and Melaque are without water or electricity, which is expected to be restored in two to three days.
The hurricane also caused flooding in the municipalities of La Huerta, Villa Purification and Autlan, while in Nayarit classes have been suspended in the municipalities of Bahia de Banderas, San Blas and Santiago Tecuala Ixcuintla.
Workers rushed to fill and stack sandbags to protect the Beach Volleyball Stadium in Puerto Vallarta on Tuesday, an official venue for the Pan American Games.
Guadalajara was also hit by heavy rain from early Wednesday morning and the rain is continuing across the south coast of Jalisco and especially now in the highlands.
Jova will gradually weaken as it passes through western Jalisco, according to the National Weather Service (SMN) forecast. Although there is some concern about the possibility of more rain affecting the early days of the Pan American Games, the worst seems to be over.
At the time of publication the State Civil Protection Agency remains on red alert in Jalisco.
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