Mercy Ali, 26, allegedly got involved in an extra-marital affair with another man, resulting in her falling pregnant.
It was alleged that she managed to conceal her pregnancy until she gave birth to a baby girl on April 30.
Ali then decided to throw the baby in the toilet as she feared her husband, who had left for South Africa in 2012.
The incident came to light after a neighbour heard the baby crying from the toilet.
The baby was taken to a nearby hospital where she was said to be recovering.
The mother would face charges of concealing her baby, in contravention of section 232 of the penal code.
This was not the first time that such an incident had been reported in Malawi.
According to News Now, A 30-year-old woman was arrested last year after she dumped her infant in a toilet.
The mother was charged with attempted murder.
The case came to light after passers-by heard the baby's cries.
- News 24