The 2013 Teens & Careers survey was co-sponsored by Junior Achievement, ING U.S. Foundation and conducted by GfK Public Affairs & Corporate Communications. The survey's margin of error is +/- 3 percent at the 95 percent confidence level. JA has been doing the survey in some format since 2002, but only polled its own members until 2009 when it switched to a national sample of randomly selected teens.
The waning interest in the STEM jobs may prove worrisome amid other reports of workforce unpreparedness.
"The info that's out there is not reaching the kids in terms of the career options that are out there for them," said Jack Kosakowski, the president and CEO of Junior Achievement USA, which trains students in workforce readiness, entrepreneurial skills and financial literacy.
Kosakowski said schools and parents need to talk to students early to make sure they don't grow up with champagne taste and only a beer budget. "Money is the new birds and the bees talk," he said.
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Nicole Smith, a research professor and senior economist at Georgetown University, agreed there is a lack of understanding among students about which majors are likely to churn out students with low earning prospects, especially if they don't continue to graduate school.
"We know where the jobs are," she said. "A lot of the young adults just don't have the available information."
Smith urged universities to make potential earnings expectations more clear to its students, even if that means "we have to talk about the majors that don't work."
STEM, health care and community service jobs will be the fastest growing occupations through 2020, but also will require high levels of post-secondary education, according to the Help Wanted report she worked on for Georgetown's Center on Education and the Workforce.
But she said it's not all about STEM. "There's still hope for the English majors," she said, noting that even Google and Apple have a lot of liberal arts majors among their ranks. They just have to rethink how to market their soft skills, such as critical thinking and inductive reasoning. "That's where liberal arts majors have the strength," she said.
The release of the Teen Survey showing less interest in STEM careers coincides with a report this week by the U.S. Census Bureau showing that women, who make up half the workforce, account for only 26 percent of STEM jobs. The Census numbers also revealed that men with a bachelor's degree in science or engineering and employed full time, year-round in STEM occupations earned $91,000 on average, compared with women who made $75,100.
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Solving the workforce problem isn't as simple as putting more career counselors in schools, as those numbers have actually gone up in recent decades. The national ratio of counselors to students has improved to 471:1 in 2011 from 588:1 in 1986, according to National Center for Education Statistics.
"While the numbers have grown over the years, so have the needs of students and the things schools are being asked to do," Jill Cook, the assistant director of the American School Counselor Association told CNBC. Ideally, that ratio should drop to 250:1, she said.
More information is available at the Department of Labor's guide to occupations and their expected income levels.
—By CNBC's Amy Langfield. Follow her on Twitter