Sheriff Jim Alderman turned to reporters during a news conference and held thumbs up and said, "He's at the house."
Alderden said an investigator on the scene saw the boy and he was fine.
He said the boy apparently has been in the attic the whole time.
The boy's brother had said he saw 6-year-old Falcon Heene get in the balloon before it took off. The flight last two hours and spanned 50 miles and set off a frantic search.
The saga captivated people around the world as they stopped to watch the jaw-dropping sight on television of the balloon gliding through the air.
The flying saucer-like balloon tipped precariously at times before gliding to the ground in a field, the culmination of a two-hour, 50-mile journey through two counties.
Larimer County sheriff's spokeswoman Kathy Messick said one of the boy's two older brothers saw 6-year-old Falcon Heene get into a box that was attached to the balloon with pegs.
The box was not found when the balloon landed; video appeared to show something falling from the balloon at some point after it launched.
The balloon was owned by the boy's parents, Richard and Mayumi Heene, who are storm chasers and also appeared on the ABC reality show "Wife Swap."
Kevin Kuretich, of the Colorado Division of Emergency Management, said authorities were searching the ground along the path of balloon.
"We're searching for the boy from the point where this took off to where it landed," Kuretich said.
He said it also had some kind of electric power unit which was run by double-C batteries. He said the balloon did seem to big enough to carry a 6-year-old. Messick also said investigators are looking into every possibility, including whether the boy was ever in the balloon. Yellow crime-scene tape was placed around the home.
Jason Humbert saw the balloon land. He said he had gotten a call from his mother in Texas who told him about the balloon. He said was in field checking on oil well when he found himself surrounded by police who had been chasing the balloon, which came to a rest 12 miles northeast of Denver International Airport.
Neighbor Bob Licko, 65, said he was leaving home when he heard commotion in the backyard of the family. He said he saw two boys on the roof with a camera, commenting about their brother.
"One of the boys yelled to me that his brother was way up in the air," Licko said.
Licko said the boy's mother seemed distraught and that the boy's father was running around the house.
In a 2007 interview with The Denver Post, Richard Heene described becoming a storm chaser after a tornado ripped off a roof where he was working as a contractor and said he once flew a plane around Hurricane Wilma's perimeter in 2005.
Pursuing bad weather was a family activity with the children coming along as the father sought evidence to prove his theory that rotating storms create their own magnetic fields.
Although Richard said he has no specialised training, they had a computer tracking system in their car and a special motorcycle.
The Heene family appeared twice on the ABC reality show "Wife Swap," most recently in February.
"When the Heene family aren't chasing storms, they devote their time to scientific experiments that include looking for extraterrestrials and building a research-gathering flying saucer to send into the eye of the storm," it says.
While the balloon was airborne, Colorado Army National Guard sent an OH-58 Kiowa helicopter and was preparing to send a Black Hawk UH-60 to try to rescue the boy, possibly by lowering someone to the balloon.
They also were working with pilots of ultralight aircraft on the possibility of putting weights on the homemade craft to weigh it down.
But the balloon landed on its own in a dirt field. Sheriff's deputies secured it to keep it in place, even tossing shovelfuls of dirt on one edge.
The episode led to a brief shutdown of northbound departures from one of the nation's busiest airports, said a controller at the Federal Aviation Administration's radar center in Longmont, Colorado.
FAA canceled all northbound takeoffs between 1 p.m. and 1:15 p.m. MDT, said Lyle Burrington, the National Air Traffic Controllers Association representative at the center. The balloon was about 15 miles northwest of the airport at that time.
Before the departure shutdown, controllers had been vectoring planes taking off in that direction away from the balloon, Burrington said.
Federal Aviation Administration spokeswoman Laura Brown said the agency tracked the balloon through reports from pilots.
Neighbor Lisa Eklund described seeing the balloon pass.
"We were sitting eating, out looking where they normally shoot off hot air balloons. My husband said he saw something. It went over our rooftop. Then we saw the big round balloonish thing, it was spinning," she said.
"By the time I saw it, it travelled pretty fast," she said.
The story gripped the television news networks, which set aside other programming to follow the balloon and speculate on the safety of the boy.
"It's got everybody freaked out," said Fox News Channel's Shepard Smith, "and why wouldn't it?"