The former Brazil star, whose arrival was announced a fortnight ago, signed an 11-month contract in front of journalists and photographers in Tokyo on Monday.
The contract is renewable every year until the 2006 finals in Germany, where Japan will be hoping at least to match their second round appearance this time around.
"It was a great result to reach the last 16, but Japan didn't have to play in the qualifying rounds," Zico said.
"We have to fight through the qualifying rounds for the next World Cup.
"So first of all, I have to form a team to play the qualifying rounds."
Zico will get his first taste of international management when the Asian champions take on China in Beijing on 22 August.
He has extensive experience of Japanese football as he has been a player and general manager at J-League champions Kashima Antlers since 1991.
And he was also Brazil's technical director at the 1998 World Cup.
One of his main priorities will be to improve the co-ordination between Japanese clubs and the national side.
Zico, who took part in three World Cup finals, admitted recently that he had initially wanted to be co-ordinator of Japan's national squad.
But the Japan Football Association preferred him to take on the coach's role.