The situation is worse in slums where infrastructure is basic. The few private and public facilities that exist charge up to USh200 [US10 cents] per use of a toilet.
"These areas are characterized by poor drainage systems and in the rainy season, the problem becomes worse," said Bernard Luyiga, a councillor in Kampala district. "We have not invested enough in this area.
"Water and sanitation in Kivulu [slum in Makerere area, which he represents on the city council] are among the worst I have come across in my life. We tried to use Eco-san toilets... but the 'flying toilet' has remained rampant."
Eco-san toilets use a natural biological process to break down human waste into a dehydrated, odourless, compost-like material, and save on water use. They were developed in South Africa in the 1990s.
It is difficult to tell how many facilities exist in Kivulu, but several pits latrines were visible, with dilapidated rusty iron sheets for walls, cracked floors and plastic roofs.
The situation is similar in other slums. About 6.2 percent of households in the city have no toilet facilities at all. Most, according to chief health inspector Mohammed Kirumira, are in the slums.
"Human waste is a problem to reckon with and many households lack a toilet, bathroom or kitchen," Kirumira told IRIN.
According to the city council: "One study conducted by Chemiphar estimated that up to 90 percent of the natural springs in Kampala are contaminated, especially in the wet season, yet this remains a major source of water for the urban slum dwellers."
Agatha Nambi, whose house stands near a drainage stream formed by an overflowing pit latrine in Kivulu, said: "It is very difficult to keep clean here. You observe cleanliness in your home, but other people just bring their mess to you and you have to give up... that is why our children keep getting sick."
Justus Namenya, a casual labourer living nearby, added: "This is the rainy season, so this place is unbearable. [It] becomes filthy and sometimes water flows up to your house with all the dirt in it."
Only about 65 percent of Kampala's two million residents have access to clean water. The rest use water that is sometimes contaminated by pit latrines.
According to Uganda's Lands, Housing and Urban Development Ministry, the high cost of piped water has forced some city dwellers to rely on springs and wells.
"Over 50 percent of household occupants in Kampala are hospitalised every three months due to malaria while contamination of water by prevalence of micro-organisms is evident in the water sources of the city," it said in a paper.
A recent survey by the Catholic Church's Justice and Peace Centre found that average toilet to household ratio in Kampala slums was about 1:25.
"The children are told to use the school toilets so that when they come back home, they do not ask for money to go to the toilet," the survey report, The plight of the urban poor and yet increased rural-urban migration, noted.
"Poor sanitation accounts for cholera outbreaks that are usually experienced in the slums of Kampala."
According to UN-HABITAT, 44 percent of Kampala's population live in unplanned, underserviced slums. Informal settlements cover up to 25 percent of the city's total area.
In informal settlements, only 17 percent of the population can access piped water. According to UN-HABITAT: "There is a high prevalence of sanitation-related diseases such as diarrhoea, worm infestations. Malaria is also endemic."
Some 92.7 percent of Kampala's population, the African Development Bank found, used on-site sanitation systems including septic tanks and pit latrines. However, emptier services, which are offered mainly by private sector on a cash-on-demand basis, were inadequate.
"As a result, effluent from latrines and septic tanks is often discharged into the environment untreated," it added.
Uganda's State Minister for Lands, Housing and Urban Development, Michael Kafabusa Werikhe, said the government was determined to address the appalling sanitation in the city.
Kampala authorities are trying to roll out a new sewage system by 2014, financed by the European Union, German government, African Development Bank and Ugandan government.
"Uganda is targeting to uplift the lives of at least one million people by the year 2020 through implementing the slum upgrading strategy and action plan," Werikhe told IRIN on 7 January.
"We believe that slums are a development challenge which must be addressed to create harmony in our societies," he added.