A Sabah Fire and Rescue Services Department spokesman said Friday that Tenom was the worst hit with more than 2,200 people evacuated.
Some 285 people from two villages in nearby Keningau were forced to leave their homes while 48 people from six villages in Beaufort were also evacuated.
Another 12 roads and bridges were cut off due to flooding or landslides, he added.
The State Government will do its level best to provide the necessary assistance to the flood victims in Sabah.
Chief Minister Datuk Seri Musa Aman said the State Disaster Committee would hand out aid including food supply and other basic necessities to those affected by the severe flooding in Beaufort, Keningau (Sook) and Tenom.
Accompanied by Minister in the Prime Minister's Department Datuk Seri Shahidan Kassim and State Secretary Tan Sri Sukarti Wakiman, Musa visited all three flood-hit areas where he also received briefings on the current flood situation.
"The government is concerned about the plight of the flood victims.
As you can see, the federal minister (Shahidan) in charge of disaster-related matters is also here to assess the severity of the flood and address what needs to be done to alleviate the situation," he said.
He said the State Disaster Committee chaired by Sukarti and the relevant authorities were closely monitoring the situation and would update the public through the existing channels including social media.
"I also ask those affected to be calm and not panic. I know it's a difficult and frustrating situation. Please also listen to the directives issued by the relevant authorities to move for your own safety. This will facilitate the evacuation process and also the channelling of assistance," he said.
Musa said he had also asked the relevant authorities such as the police, Royal Malaysian Air Force and Sabah Air to assist in transporting food supply and other basic necessities to areas not accessible by road.
"Aside from the state departments and agencies, we also welcome assistance from NGOs and generous individuals. In times of crises, we can all contribute in some way," he said.
Musa also cautioned children about playing in the flood waters and for parents to keep a close watch on them.State Assistant Minister of Agriculture and Food Industries Datuk Sairin Karno said floodwaters had receded in certain areas within Keningau and Tenom districts, although many evacuees remained in relief centres.
"The flooding was quite severe and in some places, houses were submerged to the rooftops," said Sairin, who is the Liawan state assemblyman.
He said the floodwater levels went up so rapidly that many victims had no time to save their belongings.
"Some are facing the prospects of returning to seriously damaged houses, filled with mud and damaged television sets, furniture and clothes," Sairin added.
He said Welfare Department officials trying to asses the damage were unable to reach certain areas due to the floods.
Sairin said villagers in Keningau and Tenom were bracing for more floods as rain was continuing in the Crocker Range area.