"There should be a high bar for charter approval and, in exchange for real and meaningful autonomy, there must be absolute accountability," he said, highlighting states such as Arizona, Florida, Minnesota, New Mexico, Ohio and Texas, where he said accountability is "minimal" and "unacceptable."
In 2008, 1.3 million students were enrolled in the 4,303 public charter schools operating in 40 states and Washington, D.C. -- roughly 3 percent of the amount in the nation's public schools.
The head of the nation's largest teachers union was pleased to hear Duncan's firm warnings to charters.
"They are no longer equating charters with innovation, and that was a big point for us," National Education Association president Dennis Van Roekel told ABC News Thursday. "There are a lot of charters that aren't innovative. There are a lot of public schools, non charters, that are innovative."
As the Obama administration calls for more charter schools, unions also may push for a larger role in the movement. Charter schools typically operate free from the rules inherent in union contracts and have been criticized by teachers in the past for draining resources from traditional public schools.
Last week in New York, the United Federation of Teachers and the American Federation of Teachers formalized a labor deal with Green Dot, a charter school operator, for a New York charter school in the Bronx.
"This contract can serve as a blueprint for giving charter school educators a voice, for bringing innovations to the classroom and for looking at new ways to improve labor-management relations in our schools," said AFT president Randi Weingarten.
Although the contract does not guarantee tenure to teachers, it promises that no teacher will be fired without "just cause," and it calls for a 14 percent increase in teachers' salaries above the city contract levels.
"Across the country, we are hearing from more and more educators who want the fairness and professionalism that comes with union membership and a collective bargaining agreement," said Weingarten, formerly president of the UFT.
Andrew Rotherham, co-founder and publisher of the Education Sector, a Washington, D.C., think tank, lauded those involved in the deal for making the tough decisions necessary to compromise.
"I think it's an important touchstone," he said.
But Rotherham warned that the union agreement reached with Green Dot may not apply across the board.
"I would be careful in overgeneralizing from it," he said. "Some of these other [high-performing] schools, they just aren't going to take the risk."
Duncan has underlined the involvement of unions in charters.
"Charters are not inherently anti-union," he said last week. "Albert Shanker, the legendary head of the American Federation of Teachers, was an early advocate. Many charters today are unionized. What distinguishes great charters is not the absence of a labor agreement but the presence of an education strategy built around common sense ideas: more time on task, aligned curricula, high parent involvement, great teacher support, and strong leadership."
But this may not be entirely true, Bracey noted, saying that while Shanker was an early advocate of charter schools and helped launch the movement in the late 1980s, he later jumped ship. By 1994, Shanker described charters as "a recipe for chaos."
Van Roekel predicted more union involvement in charters.
"All charters are public schools, and, depending on the state law, in some of them they are unionized," he said. "In some states they aren't allowed to. As that works through, I think you'll see more of it, not less of it."