Prisons chief Nishan Dhanasinghe said around 6,000 rice and curry parcels would be distributed to the affected.
He has told BBC Sinhala Service that all prisoners volunteered to donate their meal in that manner.
All prisoners volunteer to donate their lunch
Dhanasinghe said the food parcels would be distributed through the police.
He also said no prison or prisoner had so far been affected by the floods.
However, cooking of food at Galle and Matara prisons has become difficult, and Welikada prison will send food for both prisons, he added.