The gift broke the ice as Fukuda sat down with Bono, Microsoft Chairman Bill Gates, former British Prime Minister Tony Blair and other major supporters of more aid for Africa.
Fukuda asked the U2 frontman if his music was on the red recording device.
"No, but you can download it," said Bono.
"My son has some of your music," Fukuda told him.
After the private meeting, Fukuda told government and business leaders at the World Economic Forum that African development would be one of the three major themes of the G-8 meeting he is hosting in Japan this July.
Part of the proceeds from sales of the special-edition red iPod go directly to the Global Fund to fight AIDS, Tuberculosis and Malaria in Africa.
Earlier this week, Bill Gates said the Red-branded products have generated $50 million for the fund in the last year and a half.
