The star, who plays villain Lord Roderick in the film, described the process as "humiliating".
"I can't stand 3D, I really can't. I'm happy to go watch it but I don't work shooting in 3D. It's not fun," he said.
Tucci was nominated for an Oscar in 2009 for his role in The Lovely Bones and starred in The Hunger Games.
Brian Singer's adventure, based on the fairytale Jack and the Beanstalk, also stars Nicholas Hoult and Ewan McGregor.
Tucci said: "Nobody will tell you it's so fun shooting in 3D. We were all dressed in stupid outfits.
"It was pretty funny sitting around in chairs, everybody with little caps on, tight spandex things with little balls all over you. I'm not kidding.  It's so humiliating!"
He added: "We had a lot of difficulty with the cameras, they broke down a lot and the crew was cursing them.
"Ultimately it looks amazing and you have to be patient, but when you're sitting around for 13 hours a day in soaking wet leather doublets, and you maybe get two shots off a day, it's kind of frustrating."
The actor, who won an Emmy Award for his performance in HBO TV film Winchell and also starred in The Devil Wears Prada, said the new technology made it less interesting for actors.
"You end up doing a lot of stuff in front of green screen, that's not really very exciting for an actor," he said. "We're probably going to be replaced by digital-something soon.
"I'm hoping either I'll have enough money I won't have to worry about it at that point, or I'll be dead... They need voices for animation, but soon they'll figure that out too.
"I'll be honest, an independent film, you do it because you love it, but I think motion capture movies are the ones where you have to be paid a lot of money.
Released in the US on 1 March, Jack The Giant Slayer underperformed at the box office, taking $28m (Â£18.6m) in its opening weekend. The film reportedly cost $189m (Â£125.5m) to make.
It will be released in UK cinemas on 22 March.
Oscar-nominated actor Stanley Tucci has admitted he does not enjoy working on CGI and 3D films, despite starring in new 3D movie Jack The Giant Slayer.