"If I were to liken the history of African development to a volume of literature, then what we are about to do now is open a new page entitled the 'Century of African Growth'," he said.
Japan's fourth African development conference, following three others since 1993, has attracted more than 40 African heads of state.
Fukuda's focus on Africa comes as Japan lags behind the fast-growing economic powers of China and India in accessing the continent's rich energy and mineral resources.
Japan's trade with Africa is a meagre 2 per cent of its overall trade.
Jakaya Mrisho Kikwete, the president of Tanzania, said Japan's focus on Africa's infrastructure "resonates very well" with African leaders and people.
But he added that the Japanese government should do more to encourage trade and investment between Africa and Japan's private sector.
Citing World Bank figures, Kikwete said that between 2002 and 2004, just 0.4 per cent of Japan's $108.5bn in foreign direct investment went to sub-Saharan Africa.
To foster Japanese businesses in Africa, Fukuda said Japan would dispatch a large-scale economic mission, comprising leaders from the public and private sector, later this year.
Aiming to double Japanese private investment in Africa, the country will also offer $2.5bn in financial assistance through the Japan Bank for International Cooperation, Fukuda said.
Tokyo currently provides $1bn to Africa in official development assistance.
Japanese officials said a number of African ministers attending the Tokyo conference have voiced concerns over the impact of soaring food prices around the world.
Japan, which recently announced a $100m emergency food package, will direct much of those funds to Africa, Fukuda said.
He also urged African nations to double rice production to 14 million tons over the next 10 years, offering Japan's technical expertise to help reach the goal.
"We are deeply concerned by the fact that many African countries are in great difficulty as a result of the recent sharp rise in food prices," he said.
Global food prices have nearly doubled in three years, according to the World Bank.
Experts blame the soaring costs on trade restrictions, poor crop-growing conditions, higher energy and fertiliser tariffs and the rising production of biofuels.