About 200 people were expected to shelter at Tavua District School in the northwest of the main island, Viti Levu.
One of the school buildings still has a gaping hole in its roof after the category five Cyclone Winston tore through little more than a month ago.
The school is sheltering people from Nabuna village who have had to leave their flooded homes already damaged by Cyclone Winston, which hit six weeks ago.
The evacuation coordinator, Ratu Ovini Bokini, said people started rushing in on Monday.
"I think they're going to be staying for another two days. It depends on how the weather goes. Everywhere gets flooded now. Even during Cyclone Winston I was here with them. They were here more than a week. People have started coming in. I'm expecting 200 to come in."
There are also fears that the heavy rain and flooding in Fiji since Sunday will heighten the risk of disease in remote villages.
The Red Cross has been assessing sanitation and water supplies in villages inland from Rakiraki which were hard hit by Cyclone Winston.
A Red Cross water, sanitation and hygiene specialist, Ana Zarkovic, said many village toilets and water systems were ruined by Winston, forcing people to go to the toilet in the open, which in turn polluted the rivers and streams.
She said things were slowly being restored, reducing health risks, but she fears the heavy rain has now set some remote communities back.
"Following the rains in the last two days, there's a chance that the water supply has been damaged through the silt and the rocks and there's a risk the communities may be back to using the secondary water sources which is a bit worrying."
The United Nations Office for the Coordination of Humanitarian Affairs reports an estimated 250,000 people need help with water, sanitation and hygiene after Winston.
63,000 people have received such assistance so far.
Sugar cane growers in the northwest of Fiji's main island Viti Levu are calling for urgent assistance after the latest heavy rain and flooding.
Much of the crop in the area from Ba to Rakiraki was wiped out after Cyclone Winston and farmers say they have seen little assistance so far to help with replanting.
A farmers' representative in Tavua, Chandrika Prasad, said many farmers are surviving only with help from overseas family and friends.
He predicts up to 70 percent of the 7,000 growers in his area will walk away from sugar.
"First it was dry weather; two years, nothing. And then hurricane and then this one - rain. If you go to a farmer's house they've got no roof. Everybody's suffering."
Mr Prasad said if farmers do stay in the industry it will take them at least ten years to recover from the recent weather patterns.
The Fiji Meteorological Service said the heavy rain was likely to persist for at least the next day.
The tropical disturbance to the south of the country was only moving at about 12 kilometres an hour.
The acting director of the Meteorological Service, Misaeli Funaki, said there was already flooding in the western and northern divisions, but flood warnings are in effect for the whole country.
Mr Funaki said the heavy rain was not expected to end soon: "The whole system is anchored over Fiji, and this is going to be the case for the next - even into tomorrow and into the day after. The trough will remain slow moving over us and that will be dumping in more rain as we look ahead."
Misaeli Funaki said another tropical disturbance to the west also has the potential to develop into a weak tropical cyclone as it moved towards Fiji.
Pic: Nadi Town Courtesy Fiji Govt