The damage caused by the flooding across the country led the government to declare a three-month state of emergency last Friday.
More than 500,000 people have been affected in 17 of the country’s 18 states, the authorities say.
The 99 recorded deaths have been caused by drowning, mudslides and buildings collapsing.
The level of the Blue Nile, which is the Nile’s main tributary, has risen to 17.57m, AFP quotes the water ministry as saying.
This is the highest level since records began more than a century ago.
In Khartoum state alone, more than 100,000 people are
in need of shelter after having lost their homes.
It says that there are heavy rains forecast for neighboring Ethiopia and parts of Sudan which could lead to a rise in the level of the Blue Nile.