Metservice said in the warning that the heavy rain may cause surface flooding and slips, as well as cause streams and rivers to rise rapidly.
Horizons Regional Council, the body responsible for monitoring the Whanganui River, says that while the river was coping with the rainfall currently, there was uncertainty as to how severe the weather system will be.
"Flood flows in the Whanganui are currently well within the range of what the awa can accommodate," Horizons group manager for river management Ramon Strong said.
"While our environmental data team's models suggest this event won't cause any particular problems, there is some uncertainty as to the precise track of this weather system.
"We're also aware that soil moisture levels across the Manawatū-Whanganui region are now much higher than they were a few weeks ago. Saturated catchments, rivers and streams will respond more quickly and to higher levels with intense rainfall.
"The rain has been particularly concentrated on the Tararua Ranges and the Whanganui catchment, and that's where more rain is expected to fall."
A spokesperson at the council said that the Horizons Emergency Coordination Centre was in contact with the affected territorial authorities and is ready to respond if necessary.