The government plans to send emergency aid and shelter materials, Mahinda Samarasinghe, Sri Lanka's disaster management minister, said.
Hundreds of thousands of people in the flooded regions were already displaced by
the fighting between government troops and the rebel Liberation Tigers of Tamil Eelam (LTTE) and were living in temporary huts.
Aid agencies were evicted from the territory in September, when the government said it could not guarantee their security amid the fighting.
Offensive slowed down
The Sri Lankan government has intesified its efforts to defeat the rebels and announced on Wednesday that the fall of Kilinochchi, LTTE's political headquarters, was "imminent."
Monsoon rains have since then slowed the government forces' military offensive to capture Kilinochchi, the defence ministry said on Friday.
Officials said mine-fields had shifted following heavy rains and grounds troops had to move more cautiously.
However, fighting raged along several fronts in the north, with troops killing at least two members of the LTTE on Thursday, the ministry said.
The LTTE did not comment on the military claims, but its leader, Velupillai Prabhakaran, vowed on Thursday to fight on and push back government forces closing in on Kilinochchi.