The aid is to help rebuild houses and roads and delivery is to start in mid-September, he said, adding that transporting the supplies would cost an additional $10.6m.
The floods have led to the postponement of a landmark summit between the leaders of the two Koreas from end August to early October.
On Thursday, about 40 South Korean trucks crossed the heavily-fortified border between the two countries carrying a range of emergency relief supplies including instant noodles, as well as other food, drinking water, blankets and medicine.
|Aid agencies say rains destroyed tens of |
thousands of homes [Muhammad Khalid/IFRC]
Officials said they planned to finish that delivery by the end of the month.
North Korea battles acute food shortages even in years with good harvests, but Pyongyang and international aid agencies say rains in August brought some of the worst flooding in years that ravaged large areas of farm land.
The floods also destroyed tens of thousands of homes and buildings and left extensive damage to roads and highways.
Hundreds of people have been reported dead or missing and more than 300,000 made homeless.
Lee said North Korea was in a state of emergency, with the government and residents out in full force for recovery work.
South Korea is one of the largest donors of humanitarian aid to the North.
In the past though it has drawn criticism for distributing aid directly to its neighbour without the strict monitoring that usually accompanies international assistance to ensure it reaches those most in need.
Critics of the North Korean government say aid is often diverted to the country's huge armed forces, which often receive the pick of resources under the so-called "military first" policy.
Other international aid groups have also issued appeals for emergency aid to help North Korea.
The UN World Food Programme, which is already in the country feeding the most needy, said this week it would immediately begin the distribution of emergency food rations and launched an appeal for donations.
Other aid groups operating in the North such as the Red Cross are also providing assistance.