According to World Vision, families in rural communities are struggling to cope with the influx of people from capital Port-au-Prince, which was largely destroyed by the January 12 earthquake.
With the rainy season approaching, the Christian aid agency fears these communities could slide into deeper poverty as resources are rapidly depleted.
"Haiti's rural communities were already struggling to make ends meet before the earthquake," said Jean- Claude Mukadi, the relief response manager for World Vision in Haiti.
"Now, as people continue to arrive in these communities, joining the hundreds of thousands who have already fled, they are all looking for food, water, and shelter.
"It's critical that efforts are put into place to help the families who were already living in these areas as well as those who are displaced from their homes."
More than 40,000 have arrived in the small island of La Gonave, off the west coast of Haiti, since the earthquake, stretching the resources of the 100,000 people already living there.
World Vision fears the number of refugees could exasperate food insecurity on the island, which had a chronic malnutrition rate of 13 per cent prior to the earthquake.
"On La Gonave, the price of rice has already gone up 60 per cent. Local providers are finding it very difficult to get products because many warehouses in the capital were destroyed," said Kimcy Blaise, World Visions Regional Coordinator for La Gonave.
"We are worried that the increased food needs on the island will result in children and families going hungry because they simply can't afford basic staples anymore."
World Vision was working with local government leaders prior to the earthquake to construct water community tanks. The aid agency is in a race against time to repair fifty water cisterns rendered unusable by the earthquake, before the rainy season arrives.
More than half a million people have left Port-au-Prince in search of alternative accommodation. World Vision's post-quake assessment of La Gonave found that the number of people per household had increased as much as fourfold.
"World Vision has been doing rural development work in Haiti for many years, and while it is necessary to provide relief to displaced families in Port-au-Prince, it is critical to remember those living outside the city," said Mukadi.
"If more resources are not channeled to the rural communities, the poor will be forced to return to the capital city, adding to the already overcrowded conditions there."