In an interview he said he is not calling for capping enrollment in existing charter schools.
"We are simply saying there should not be any more new schools" until the flaws are fixed, he added.
The Pennsylvania Coalition of Public Charter Schools blasted Wagner's report and called it "an attack on Pennsylvania families' right to public school choice."
Executive director Guy Ciarrocchi said charter schools receive less funding per student than district schools.
"The only financial problem that needs to be fixed is that charter schools need more support, not less," Ciarrocchi said.
As a state senator, Wagner voted for the state's 1997 charter school law. But he said the current funding system is "a bad deal" for taxpayers.
"The big problem is that we are trying to finance 21st Century education with 19th Century funding methods," he said.
"With Pennsylvania still mired in its greatest economic downturn since the Great Depression, we can't afford to be wasting precious financial resources on schools whose costs have absolutely no basis whatsoever on what is actually needed to educate children."
The current system, which is based on school district funding formulas, results in districts paying different rates for students at the same charter school.
He said pointed to a charter school in Homestead, Allegheny County, which draws students from 10 districts. Clairton City School District paid $11,337 for each of its students while the East Allegheny School District pays $7,201 per student.
The state auditor general also said that although it costs less to educate students in cyber schools, the cybers receive the funding as traditional charter schools.
Wagner called on the Legislature to develop a standardized funding system for charters and urged the state Department of Education to take a more active role in charter school oversight.
He had called for similar changes in 2007.
Wagner, who ran unsuccessfully in the Democratic primary for governor in May, said he hoped his report would serve as a "bell ringer" that would spur state government to act.
Contact staff writer Martha Woodall at 215-854-2789 or at firstname.lastname@example.org