"We will 5.6 billion rupees to make emergency repairs to bring the roads to a motorable condition," Pemasiri said.
"But the fully rehabilitate the roads we will need about 50 billion rupees."
He said RDA engineers were still assessing the damage with some areas still under water, but repair work has started and the agency hopped to complete emergency repairs within a few weeks.
The agency will use funds already allocated for maintenance and ask the Treasury for additional supplements.
"But to fully rehabilitate those road we will need about 50 billion rupees," Pemasiri said.
"We are exploring possibility of getting donor funds."
The Asian Development Bank, World Bank and China are the top funders of Sri Lanka's roads, with the European Union also giving grant funding for roads especially in the Eastern province following the 2004 tsunami.The damaged roads were mostly in the Uva, Eastern, North Central and North Western provinces of the island.
Pemasiri said road rebuilt in recent years had withstood the floods well, except in the Trincomalee district where Sri Lanka's longest river the Mahaweli falls in to the sea.
Water rushing to the sea has carved new paths through the land damaging roads in several areas, he said.
Irrigation officials said earlier that from December 15 through January many areas had received three to four times the normal rainfall and some reservoirs had spilled more than ten times their normal capacity, while some spilled for the first time in more than a decade.
Officials say in January torrential rains hit the island twice in close succession flooding land which had been already saturated and spilling over reservoirs which were already filled.
Irrigation authorities have said that about five billion rupees would be needed to make emergency repairs mostly to the canal system, bringing the total repair bill to the Sri Lanka taxpayer close to 60 billion rupees, not counting the cost of private residences.
Corrected - damaged areas also include eastern province