The district, in its statement, said the expansions would have added $500 million in charter costs to the district over the next five years.
As the school system struggles to find a way to deal with its projected deficit, principals of district-run schools have been told their budgets will be slashed by 25 percent for the fiscal year that begins July 1.
District officials said they met with charter operators Thursday to inform them of the recommendation to the School Reform Commission.
The announcement came 10 days after more than 250 charter students and supporters rallied in front of the district's headquarters at 440 N. Broad St. to call for charter expansions.
Naomi Booker, president of Philadelphia Charter Schools for Excellence, which organized the rally, said she was not surprised by the decision.
"We're in favor of adding seats," she said. "We're trying to do what is right for the children of Philadelphia. At this point, this is the decision that the School District has made, and we will go along with it. We really need to work on this issue of how education is funded in the city of Philadelphia."
Booker, chief executive of Global Leadership Academy Charter School in West Philadelphia, said she expected charter operators will work with the district to press the legislature to increase education funding.
She said the district had said it expected to authorize charter expansions in 2014-15.
Mark Gleason, executive director of the Philadelphia School Partnership, said: "I think this decision is one that doesn't make anybody happy - not the district, not the charter schools, and not the families."
But he said it was clear that the district does not want to spend money that it doesn't have.
"I think everybody understands that this is a real budget crisis. What this underscores is that the solution to the crisis needs to be one that involves all parties."
District officials said they intended to revise the district's five-year financial plan to find money to support charter expansions in the future.
"We do not anticipate being in this situation forever," Deputy Superintendent Paul Kihn said in the statement, adding that the district planned to continue expanding high-performing schools.
A redesigned process will allow only high-achieving charters to apply to add students.
The district said it also would urge the SRC to move quickly to turn around or close poorly performing charter schools as it has done with troubled district schools.
Last year the SRC approved expansions of 14 charter schools that will add 5,416 seats by 2017.
The 84 charter schools in the district enroll more than 55,000 students.
Contact Martha Woodall at 215-854-2789 or 215-313-3477.