Rising floodwaters threaten some 9,000 people in Mozambique's central Zambezia province and those living near swollen rivers have evacuated their homes, emergency services said on Wednesday.

"Around 9,000 people are at risk in the lower Licungo...the river has already flooded some villages," a spokesperson for the National Disaster Management Institute, Rita Almeida told AFP.

The central Sofala is so far the worst affected after the Pungoe River burst its banks late last week, cutting road access between Beira, the country's second largest city and Zimbabwe.

People living near the Licungo River Basin near the coast have left the area voluntarily to seek shelter in temporary camps set up during the 2013 flood season.

Rescue teams are expected to begin combing the coastal zone close to the town of Nante on Thursday for anyone left behind.

"Tomorrow we want to do some fly-overs to see if there are any people left," Almeida said.

Mozambique's rainy season which runs from October to April is currently at its peak.

Heavy rainfall is still being recorded in the coastal Zambezia province as well as the northern Nampula and CaboDelgado provinces.

Coastal Mozambique is home to nine international river basins, making it especially vulnerable to flooding.

In 2000, the country was devastated by floods that killed more than 800 people.