The government has urged many people to immediately seek higher ground.
Kenneth came just six weeks after Cyclone Idai ripped into central Mozambique and killed more than 600 people.
The UN says the remnants of Kenneth could dump twice as much rain as Idai did. It was the flooding after Idai that caused most of the deaths.
Nearly 700 000 people could be at risk in the largely rural region, many already exposed and hungry.
The United Nations says houses have begun collapsing in the north of Mozambique due to severe flooding following Cyclone Kenneth which hit the region on Thursday killing five people.