A search and rescue team deployed after the 7 p.m. twister had to cut their way through branches and debris to reach the camp where the 93 boys, ages 13 to 18, and 25 staff members were attending a weeklong leadership training camp.
"All of the buildings are gone; most of the tents are gone; most of the trees are destroyed," Lloyd Roitstein, president of the Boy Scouts of Mid-America Council, told CNN. "You've got 1,800 acres of property that are destroyed right now."
All of the children had been accounted for late Wednesday, said Russ Lewrenson of the Mondamin Fire Department.
At least 40 people who were injured in the storm were being taken to area hospitals, said Iowa Homeland Security spokeswoman Julie Tack. Most of the kids who were hurt were out on a hike when the tornado hit, Lewrenson said.
"Based on what we were seeing on radar it looked like it could have been a very powerful tornado," said Daniel Nietfeld with the National Weather Service.
The ranch about 40 miles north of Omaha, Neb., includes hiking trails through narrow valleys and over steep hills, a 15-acre lake and a rifle range.
Gayle Jessen of Fremont, Neb., said her 19-year-old son Zach is a staff leader at the camp. He called his parents to say he had a bruise on an arm and was being treated at a hospital.
"I'm so relieved my son is OK," Jessen said. She said her husband was headed to the hospital to pick up their son.
Lewrenson said parents will be reunited with their children at an undisclosed location.
David Hunt, chairman of the Mid-America Boy Scout Council's Goldenrod District, which covers several eastern Nebraska counties, said he believed the boys were from eastern Nebraska and western Iowa.
The tornado touched down as Iowa's eastern half grappled with flooding in several of its major cities. The storm threatened to stretch Iowa's emergency response teams even further.
Tack said officials were confident that the state's emergency response teams could handle the crisis because western Iowa had been largely unaffected by the recent flooding.
Tornadoes also touched down in southern Minnesota and eastern Nebraska.
A tornado ripped a house from its foundation, leaving a bathtub protruding from a back wall near Fulda, Minn., 140 miles southwest of Minneapolis. A woman inside at the time suffered a knee injury.
Another struck a farm near Springfield, Minn., causing extensive damage to outbuildings, but causing no injuries to people or livestock.
Other tornadoes in Minnesota damaged trees, pushed a manufactured house off its foundation and knocked down outbuildings.
There were no immediate reports of damage from the Nebraska twisters, though a lightning strike knocked out radar at the National Weather Service's office in Valley, about 30 miles northwest of Omaha.
From Wisconsin to Missouri, officials in the storm-ravaged Midwest on Wednesday were fortifying levees with sandbags, watching weakened dams and rescuing residents from rising water.
But Iowa was bearing the brunt of it. Inmates in black-and-white striped uniforms were rescued from a jail by boat as the raging Cedar River flooded Vinton and forced evacuations in Waterloo.
"Everything is flooded - everything is up to knee-high," said Patrice Calhoun, of Waterloo, Iowa, who rolled up her pants and waded through water to get home Wednesday morning. "You could actually swim in it."
Officials in Wisconsin were monitoring dams and high water in Indiana burst a levee, flooding a vast stretch of farmland. In Minnesota and North Dakota, strong winds closed a highway and even sent a cow into the air, a witness said.
Along the Mississippi River in Missouri and Illinois, the National Weather Service was predicting the worst flooding in 15 years. Outlying areas could be inundated, but most of the towns are protected by levees and many low-lying property owners were bought out after massive flooding in 1993, officials said.
In southeastern Illinois, floodwaters knocked out the water supply to Lawrenceville, a city of 4,600, and to a nearby state prison Wednesday morning. Officials said it remained unclear what made the city's water main stop working and they would have to wait for floodwaters to recede find the problem.
On the East Coast, officials revealed the weekend heat wave had claimed 17 lives. Most of the victims were elderly. Eight died in Philadelphia of heat-related causes, six others in New York City, two in Maryland and one in the Philadelphia suburb of Pottstown.