Honda's move has been criticised by some who feel that his mid-season move will hinder his World Cup preparations.
Zaccheroni, who has won the Serie A with Milan, felt there was enough time for the player to settle down at the new club.
"It's a good time for him to go to Milan because there are still six months to go to the World Cup," Zaccheroni told reporters in Tokyo.
"He has plenty of time to find his position and the harmony with other players. I know Honda well, he has the physical strength, the technique, everything.
"I managed Milan for three years and I'm sure it will work out for him. He will love the team and be very motivated. He will come back to us at the end of May for the World Cup in good shape."
Honda is known to be a good reader of the game with hot dribbling skills and boasts a strong scoring record with his prowess at set pieces.
Japan are the lowest-ranked side drawn in Group C for the World Cup which also has Ivory Coast, Greece and Colombia.
Having impressed in the recent friendly matches against Belgium and Netherlands, the 60-year-old coach said his team will be no pushovers.
"Japan had been improving even before I got here," the Italian who took over the reins of Japan after the last World Cup, said.
"The Japan Football Association has set a goal of winning the World Cup by 2050, but I think they will achieve that much earlier."
The Blue Samurais stunned many during the 2010 World Cup in South Africa when they advanced past the group stages with wins over Cameroon and Denmark.
Zaccheroni said he will not hesitate to tinker with his line-up ahead of the World Cup to pick a best possible 23-man squad for next year's showpiece event.
"Eight of us on the technical committee will check up on all the players domestic and abroad," he said. "I recently showed I can change teams, and I'm not afraid to keep doing it if it makes us better.
"If someone we haven't called up yet comes on strong, then I won't hesitate to pick them."
(Writing by Sudipto Ganguly; editing by Pritha Sarkar)
