Tom McGrath has discovered that kids believe Skipper, the tough, no-nonsense penguin he first voiced in the 2005 animated hit “Madagascar,” is real.

“That is the curse of being a voice,” said McGrath, who reprises the bird with a penchant for Cheezy Dibbles in the 3-D animated comedy “Penguins of Madagascar.”

When he’s performed the voice of Skipper for kids, said McGrath, “they get really scared. It’s like a theme park character taking off their costume head. It breaks the fantasy. So I have to go behind a door and do it!”

The soft-spoken, personable McGrath, 50, was never supposed to play Skipper. He’s not even an actor but one of DreamWorks Animation’s top filmmakers. He and Eric Darnell co-directed “Madagascar” and the two sequels. He went solo as a director with 2010’s “Megamind.”

McGrath had grown up watching movies starring tough guys John Wayne, Charlton Heston and Robert Stack and envisioned Stack (“The Untouchables,” “Unsolved Mysteries”) as the voice of the leader of the very comical squad of stealth penguins.

McGrath and Darnell finally got the greenlight in 2003 to hire Stack. “Unfortunately, he passed away,” said McGrath at DreamWorks in Glendale, where he’s in production on the animated film “Boss Baby,” set for release in 2016.

McGrath, who also co-wrote the first two “Madagascar” films with Darnell, had recorded the voice in a so-called preliminary scratch-track. “People were used to me doing that voice. We knew it worked when we screened it.” And it wasn’t long before DreamWorks Chief Executive Jeffrey Katzenberg told him, “You got the part, kid.”

He’s not the only animation director playing one of the wily penguins. Chris Miller, who directed the 2011 “Puss in Boots,” is Kowalski, the brains of the group, and animation editor Christopher Knights is the adorable young Private, who wants to be more than a mascot. Rico, the demolitions expert of the squad, is mute.

Though they were relatively minor — but pivotal — characters in “Madagascar,” the penguins proved to be comedic superstars. Not only were they featured in the sequels, they also starred in their own popular Nickelodeon series, “The Penguins of Madagascar.”

“These are little guys with big personalities,” said McGrath, adding with a smile, “they are guys who see the world in black and white. Every movie, people liked the penguins best because they were pure comic relief.”

It was inevitable that they would get their own movie. “Penguins of Madagascar” finds the penguins working with an elite undercover group called the North Wind, which helps animals that can’t help themselves. Their mission is to thwart the evil Dr. Octavius Brine, who bears a deadly grudge against all penguins. Benedict Cumberbatch plays the leader of the North Wind, John Malkovich is Brine, and director Werner Herzog has a voice cameo. Darnell and Simon J. Smith directed the spy comedy.

McGrath was surprised to discover just how Skipper has evolved since “Madagascar.”

“It’s a lot more jovial now,” he said. “The character was really dry and really straight in the first one. All he did was bark orders. I think a lot of, like, a poor man’s Charlton Heston kind of creeped in over the years. You’ve got this smarmy guy who is kind of like all swaggery and stuff.”