(Read More from CNBC: Plan on Working Past Age 65? You'll Have Company)
The non-profit certificate holders can also place employees in outside, for-profit workplaces including restaurants, retail stores, hospitals and even Internal Revenue Service centers. Between the sheltered workshops and the outside businesses, more than 216,000 workers are eligible to earn less than minimum wage because of Section 14 (c), though many end up earning the full federal minimum wage of $7.25.
When a non-profit provides Section 14 (c) workers to an outside business, it sets the salary and pays the wages. For example, the Helen Keller National Center, a New York school for the blind and deaf, has a special wage certificate and has placed students in a Westbury, N.Y., Applebee's franchise. The employees' pay ranged from $3.97 per hour to $5.96 per hour in 2010. The franchise told NBC News it has also hired workers at minimum wage from Helen Keller. A spokesperson for Applebee's declined to comment on Section 14 (c).
Helen Keller also placed several students at a Barnes & Noble bookstore in Manhasset, N.Y., in 2010, where they earned $3.80 and $4.85 an hour. A Barnes & Noble spokeswoman defended the Section 14 (c) program as providing jobs to "people who would otherwise not have [the opportunity to work]."
Most Section 14 (c) workers are employed directly by nonprofits. In 2001, the most recent year for which numbers are available, the GAO estimated that more than 90 percent of Section 14 (c) workers were employed at nonprofit work centers.
Critics of Section 14 (c) have focused much of their ire on the nonprofits, where wages can be just pennies an hour even as some of the groups receive funding from the government. At one workplace in Florida run by a nonprofit, some employees earned one cent per hour in 2011.
"People are profiting from exploiting disabled workers," said Ari Ne'eman, president of the Autistic Self Advocacy Network. "It is clearly and unquestionably exploitation."
Defenders of Section 14 (c) say that without it, disabled workers would have few options. A Department of Labor spokesperson said in a statement to NBC News that Section 14 (c) "provides workers with disabilities the opportunity to be given meaningful work and receive an income."
Read More from NBC News:
Terry Farmer, CEO of ACCSES, a trade group that calls itself the "voice of disability service providers," said scrapping the provision could "force [disabled workers] to stay at home," enter rehabilitation, "or otherwise engage in unproductive and unsatisfactory activities."
Harold Leigland, however, said he feels that Goodwill can pay him a low wage because the company knows he has few other places to go. "We are trapped," he said. "Everybody who works at Goodwill is trapped."
Leigland, a 66-year-old former massage therapist with a college degree, currently earns $5.46 per hour in Great Falls.
His wages have risen and fallen based on "time studies," the method nonprofits use to calculate the salaries of Section 14 (c) workers. Staff members use a stopwatch to determine how long it takes a disabled worker to complete a task. That time is compared with how long it would take a person without a disability to do the same task. The nonprofit then uses a formula to calculate a salary, which may be equal to or less than minimum wage. The tests are repeated every six months.
Leigland's pay has been higher than $5.46, but it has also dropped down to $4.37 per hour, based on the time-study results.
He said he believes Goodwill makes the time studies harder when they want his wage to be lower.
"Sometimes the test is easier than others. It depends on if, as near as I can figure, they want your wage to go up or down. It's that simple," he said.
His wife, Sheila, 58, spent four years hanging clothes at the Great Falls Goodwill for about $3.50 an hour. She said the time study was one of the most degrading and stressful parts about her job. "You never know how it's going to come out. It stressed me out a lot," she said.
(Read More from CNBC: Fed Shakes Up Global Markets as US Interest Rates Rise)
She quit last summer when she returned to work after knee surgery and found that her wage had been lowered to $2.75 per hour, a training rate.
"At $2.75 it would barely cover my cost of getting to work. I wouldn't make any money," she said.
Harold said he believes Goodwill can afford to pay him minimum wage, based on the salaries paid to Goodwill executives. While according to the company's own figures about 4,000 of the 30,000 disabled workers Goodwill employs at 69 franchises are currently paid below minimum wage, salaries for the CEOs of those franchises that hold special minimum wage certificates totaled almost $20 million in 2011.
In 2011 the CEO of Goodwill Industries of Southern California took home $1.1 million in salary and deferred compensation. His counterpart in Portland, Oregon, made more than $500,000. Salaries for CEOs of the roughly 150 Goodwill franchises across America total more than $30 million.
Goodwill International CEO Jim Gibbons, who was awarded $729,000 in salary and deferred compensation in 2011, defended the executive pay.