Greater awareness, broader definitions and spotting autism in younger children may explain some of the increase, federal health officials said.
"The concern here is that buried in these numbers is a true increase," said Dr. Thomas Insel, director of the National Institute of Mental Health. "We're going to have to think very hard about what we're going to do for the 1 in 100."
Figuring out how many children have autism is extremely difficult because diagnosis is based on a child's behavior, said Dr. Susan E. Levy of the Children's Hospital of Philadelphia and a member of the American Academy of Pediatrics subcommittee on autism.
"With diabetes you can get a blood test," said Levy. "As of yet, there's no consistent biologic marker we can use to make the diagnosis of autism."
The new estimate would mean about 673,000 American children have autism. Previous estimates put the number at about 560,000.
CBS News medical correspondent Dr. Jennifer Ashton reports that boys are four-times more likely than girls to be diagnosed with autism disorders.
Some experts say the term "autism" is overused, reports Ashton, but view the increased awareness as a positive.
"Maybe the label 'autistic specrum disorder' is correct, maybe it's not - however, if we identify that there is a need, that means we're going to do intervention," Dr. Max Wiznitzer told CBS News.
One of the studies stems from the 2007 National Survey of Children's Health. The results were released Monday, and published in October's Pediatrics.
In that study, based on telephone surveys, parents reported about 1 in 91 children, ages 3 to 17, had autism, including milder forms such as Asperger's syndrome.
The other government estimate has not been formally released yet. But because of the new published findings, officials from the Centers for Disease Control and Prevention decided to announce Friday during an embargoed press briefing that their preliminary findings also show about 1 in 100 children have the disorders.
The CDC uses an in-depth method for its estimate, said CDC researcher Catherine Rice. An agency network reviews the education and health records of 8-year-old children in selected cities and determines whether the children meet the diagnosis. Autism experts generally consider this method more rigorous than a telephone survey.
President Obama has made autism a priority for research, Insel said. Federal stimulus money has been earmarked for autism, and a 2006 law pumped millions of dollars of new federal money into autism research, screening and treatment.
The published findings, which include state-level data, will help the government plan new services, said Michael Kogan, a researcher with the federal Health Resources and Services Administration, who led the new study, which lists authors from several government agencies, including CDC.
The findings are based on the results of a national telephone survey of more than 78,000 parents of children ages 3 to 17. The survey dealt with many health issues and included two questions on autism.
Parents were asked whether they'd ever been told by a doctor or other health care provider that their child had autism, Asperger's syndrome, pervasive developmental disorder or other autism spectrum disorder.
If the parent said yes, they were asked if their child currently has autism or an autism spectrum disorder. "Yes" to both questions was counted as a child with an autism disorder.
The survey questions were flawed, said autism researcher Irva Hertz-Picciotto of the University of California, Davis. A broad definition, read to some parents who asked for clarification, didn't include "repetitive behaviors," Hertz-Picciotto said. And parents weren't asked about a professional diagnosis in the second question.
Children with autism can have trouble communicating and interacting socially. They may have poor eye contact and engage in repetitive behavior such as rocking or hand-flapping.
"The wording and definition invited much broader interpretation," Hertz-Picciotto said, and researchers didn't check what parents said against medical records.
In another finding, nearly 40 percent of the children ever diagnosed with autism disorders didn't currently have autism, the parents reported. That rate is much higher than ever found by autism recovery researchers. Outside experts said they doubt it reflects a true rate of recoveries. Autism could have been suspected and later ruled out for some of the children, the authors wrote.
One of the new study's authors was supported in part by a grant from the advocacy group Autism Speaks. The others work for federal agencies.
"Autism is a highly prevalent disorder," said Geraldine Dawson, chief science officer of Autism Speaks. "We're looking at a major public health challenge."
For more information about autism, check out these Web sites:
American Academy of Pediatrics
Centers for Disease Control and Prevention autism page
Health Resources and Services Administration (HRSA)