"With the floods, people's toilets have been washed away and most people have no access to safe drinking water," health services director Storn Kabuluzi told AFP, saying the country faced an "immediate danger" of surging cholera cases.
The cholera outbreak, which began last year, infected more than 30,600 people and claimed more than 1,700 deaths.
Malawi was already battling its deadliest cholera outbreak on record when the storm landed last week, causing mudslides and flooding, killing 476 and displacing nearly half a million.
After a record-breaking rampage, the storm caused 579 deaths in three southern African countries including Mozambique and Madagascar.
Malawi was hit the hardest as Freddy triggered floods and mudslides that swept away homes, roads and bridges - also causing massive damage to the country's water infrastructure.
"In the face of crisis and chaos, it is children who are the most vulnerable," warned UNICEF regional director for eastern and southern Africa, Mohamed Malick Fall.
In neighboring Mozambique, the interruption in water, hygiene services and sanitation "is driving a rapid acceleration in cholera case numbers", said UNICEF.
Flooding and damage caused by Freddy in the two neighboring countries have hampered access to health and other basic services, which will almost certainly exacerbate the cholera outbreaks they are experiencing, said UNICEF.