Aso chose Tokyo's Akihabara district, a noted centre for Japan's comic book subculture, for his first street speech after taking office in September, hailing comics and complaining he could not find enough time to read them.
Miyazaki said Japan should create a proper environment for children rather than building bridges and roads to stimulate the economy.
He warned Japanese children today were surrounded by virtual reality such as television, video games and e-mail.
"I feel a big contradiction as what we are doing may be depriving children of their power," he said. "But I want to continue this job, believing it is also a happy experience that a child has an unforgettable movie."
Miyazaki, whose 2001 film "Spirited Away" won the Academy Award in 2003 for best animated feature, urged Japan to liberate itself from nationalism.
"Nationalism stems from the belief that multi-ethnicity causes problems of the world.
"We learned from the last war that the town we love or the country we love can always turn into something bad to the world. I believe we must not forget what we learned," he said.
Japan's air force chief Toshio Tamogami was sacked recently after writing an essay in which he denied the country was an aggressor in World War II and said Asian countries "take a positive view" of Japan's past militarism.
Miyazaki has scored another box-office hit this year with "Ponyo on the Cliff by the Sea", a story of a fish-girl and a human boy.
He is one of Japan's biggest cultural exports thanks to his films, which include "Howl's Moving Castle" (2004), "Princess Mononoke" (1997) and "My Neighbor Totoro" (1988).