Falcon said little during the family's "GMA" appearance, briefly running off camera to vomit several times, a side effect of his asthma, Heene explained.
But his older brother, Brad, who initially alerted his parents that he thought his younger brother might have been in the balloon, said that he was "really scared" and feared Falcon might be electrocuted if the balloon hit power lines.
Home video released by the family shows Richard Heene visibly upset as the balloon lifted into the air, its tethers not properly secured. Then, the family said, it learned it might have had precious cargo.
"I just saw him go under the flying saucer," Brad said. "I saw him go under it and the door shut."
Heene and law enforcement officials told reporters Thursday that Falcon had retreated to his hiding space after his father scolded him for fiddling with the experimental aircraft tethered in the family yard.
"I was in the attic, and he scared me because he yelled at me," Falcon told reporters. "That's why I went in the attic."
"I'm really sorry I yelled at him," Richard Heene said, standing with his wife and three sons. "He scared the heck out of us."
But some of Richard Heene's former colleagues have raised questions about his parenting and accused the amateur inventor of intentionally launching the balloon in an effort to gin up publicity.
"I believe that Richard had a plan to send this craft aloft," said Scott Stevens, who used to work as a "storm chaser" with Heene. "Whether it was to leave the illusion that there was a boy on board, I don't know. [But] I believe it was a premeditated launch."
Stevens told "GMA" he stopped working with Heene because he objected to Heene bringing his children along in dangerous situations.
"I just thought he was beginning to push [his children] into some things that were ethically on the edge," Stevens said. "I knew at some point he would create a situation that would bring attention like he's having right now. I didn't want to be a part of that," Stevens said.
Heene, a former weatherman, said he built the 20-foot-long, dome-shaped aircraft for commuter travel.
"We were working on an experimental craft -- I call it the 3D LAV, a low-altitude vehicle for people to pull out of their garage and hover above traffic for about 50 to100 feet," Heene said later. "It's still the very early stages of the invention."
As millions of other people watched live video footage of the balloon on TV, many of them thinking Falcon was inside, the aircraft appeared to visibly deflate, spin and rock from side to side. When it landed near the Denver airport, sheriff's officials tethered it to the ground and cut it with sharp tools to deflate it.
But they reported no sign of the boy or a box that had been attached to the balloon.
Believing Falcon may have fallen out of the aircraft, investigators searched a miles-wide area looking for him.
Volunteers walked through the treeline near the family's home, calling out the boy's name.
"Falcon is a great kid, very adventurous, and has no fear factor," neighbor Tina Sanchez said. "For him to climb into this balloon would not be out of character."
ABC News' Michael James and Clayton Sandell contributed to this report.