Papayas are grown in tropical regions of the world, sometimes in arid regions, sometimes in very humid regions. While root rot is a problem in either area, humid regions are particularly problematic for gardeners and farmers who are trying to prevent or control soil-borne diseases. The Komohana Research and Extension Center in Hawaii recommends an integrated pest management program that includes fungicides along with crop rotation.
Papayas are highly susceptible to Phytophthora root rot and Pythium root rot. This generally occurs when the papaya is planted in infested soils, the root zone is watered too frequently, or when the plant has suffered freeze damage. These microbes damage and kill roots, causing the eventual mortality of the entire plant, especially seedlings.
The best option is to plant the tree in areas where the microbe doesn't exist in the soil. But this is a rare case, as all areas where papaya is grown currently have these microbes in the soil already. The second best choice is to rotate papayas with a crop or cover crop (green manure) that is not a viable host for these diseases, so that the population in the soil drops.
A number of fungicides can be used to treat root rot. However, most of them are either not certified for organic use, cannot be used within a certain time period before papaya harvest, or the diseases have been known to build up a resistance to them. Some fungicides are useless once the papaya tree has become infested.
Almost all approaches to root rot control are preventive measures. Rotating the crop only prevents the next papaya crop from becoming infected. Many species of Phytophthora can live in moist soil for up to six years. Neither type of root rot survives this long in dry soils, so planting a rotation crop with minimal water requirements (and thus little outside irrigation) can reduce the presence of these diseases better than planting a crop with high water requirements.
If you try to grow papayas in an area where annual precipitation is very high, it is unlikely that any form of root rot prevention will keep your papayas safe. The alternative in this area is to grow papayas in a greenhouse, and carefully control the amount of water that papayas receive. Let the soil dry out a bit between watering, and rotate with a crop that is not a host for Phytophthora or Pythium even if there are no signs of infection in your current papayas.