"I'll talk after I pitch," said the right-hander, who will come off the six-game suspension he received for an outburst last week and start against the Braves on Thursday night at Turner Field.
When pressed, Zambrano didn't budge.
"I don't have anything to say," he muttered while moving away. "What do you want me to say?"
Cubs manager Lou Piniella met with Zambrano for about five minutes behind closed doors on Tuesday to discuss the missed flight.
Piniella wouldn't comment on Wednesday, saying only: "It's been handled internally."
Zambrano, who can work out before games while suspended, traveled to Atlanta on his own, apparently without permission. It could not be confirmed whether or not he had been fined for missing the team flight.
That Zambrano had missed the flight and was called on the carpet by Piniella was first reported by The Chicago Tribune.
This isn't the first time Zambrano has run afoul of team rules. But it comes while he is on a six-day MLB suspension for his wild outburst after a close play at the plate against Pittsburgh on May 27 at Wrigley Field.
Zambrano didn't appeal his suspension and told the media last week that he was sorry for what he had done.
"I know I did something that disrespected MLB, and I apologize," he said.
Guy Curtright is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.