Days of heavy rains last week put most of Tabasco state under several feet of water, in one of the largest natural disasters in recent Mexican history.
About 80,000 people from the flooded city of Villahermosa have taken shelter in schools, churches and a multi-storey parking garage.
Standing water from the flooding attracts mosquitoes, which can carry infectious diseases such as dengue, while cholera is transmitted by contaminated water.
"We're worried about the flies now that pools of water have formed," said Leticia Frias, who has sheltered in a wooden hut at the roadside for the last eight days after her home was flooded.
Francisco Ramirez, the interior minister, said waterlogged areas would be treated in the next few days to reduce the risk of diseases.
"They will be beginning work in the next few days to fumigate all the areas that are now under water," Ramirez told a news conference in Villahermosa on Wednesday evening.
The floods, caused by rivers overflowing after heavy rain, killed at least three people and damaged about $655m worth of crops, homes, businesses and infrastructure.
A further four people were killed, and 21 others were missing, in the remote village of Juan de Grijalva, in neighbouring Chiapas state, after the village was hit by a huge mudslide more than one kilometre long.
Rescue workers on Wednesday continued to search for the missing people, digging through the mud from the landslide.
Much of downtown Villahermosa was still under water and thousands of people lined up to receive food handouts.
The government is planning a mass grave for the thousands of cows, sheep and other livestock killed in the flooding across the rural areas of the state.
In recent days, army and government doctors have given thousands of injections against hepatitis and tetanus.