The other 74 charter schools in the city made contributions on time.
"In recent history, we haven't had any issues with the school district itself," said Evelyn Tatkovski, spokeswoman for the Pennsylvania Public School Employees' Retirement System (PSERS). "But it's not unusual for there to be several charter schools on the list."
During 2012-13, the district shouldered $1.3 million in pension payments for 22 charter schools.
"We consider it to be a significant burden on the district to go through this process any time it happens," said district spokesman Fernando Gallard. "That is, of course, aside from having charters not following what is required under the law."
He said failing to make pension payments could be a sign of wider financial problems for the charters. The district looks at PSERS record when charters are facing renewal.
The state Department of Education notifies the district when charters are delinquent on pension payments and trims the district's share of state funds to cover them.
The district, in turn, reduces the charters' monthly payments to recoup the money, Gallard said. The gap between the time the state acts and the district docks charters is usually 10 days.
Records The Inquirer obtained from the district under a right-to-know request show that some charters owed a few thousand dollars and others much more.
Universal Creighton missed two pension payments totaling $267,069 this academic year. Since 2012, the nonprofit Universal Cos. Inc. has run the former district school in Crescentville as a charter.
Shahied Dwan, Universal's top financial officer, cited cash-flow issues in the year's first half when the school buys supplies.
He wrote in an e-mail that funding usually balanced out later in the year.
Ad Prima, with campuses in Overbrook and Frankford, missed a $117,938 pension payment this school year and three totaling $68,423 in 2012-13.
Attorney Scot R. Withers said there was an inadvertent oversight by Ad Prima's finance department, which underwent change. He said in an e-mail that "during this process, submitting the PSERS reports was overlooked." Future payments, he said, would be on time.
Ad Prima, which is up for renewal, is one of three city charters founded by Dorothy June Brown, who is awaiting a retrial on federal fraud charges. In January, a jury acquitted her of six counts and deadlocked on 54 others.
Laboratory - another Brown charter - failed this year to make a $102,732 payment to PSERS.
West Philadelphia's Harambee Institute of Science Technology Charter School, whose former chief executive was recently sent to federal prison for embezzlement, missed one payment this year and two last year with a combined total of $133,664.
Caren Ishmael, Harambee's chief academic officer, said fluctuating enrollment caused cash-flow problems. The school adjusted its budget and has made its recent payments.
Delaware Valley Charter High School in Ludlow and Wakisha Charter School in North Philadelphia missed multiple pension contributions. Officials at the two schools declined to comment.
Delaware Valley failed to make contributions of $124,565 this school year and $200,367 last year. Wakisha missed three pension payments this year and last total ing $300,392.
Records show Arise Academy Charter High School in West Oak Lane did not make three contributions in 2013-14 with a combined total of $43,658.
Roberta Trombetta, acting chief executive, blamed a glitch. She said Arise's checks were not credited in time because PSERS had switched to an electronic system.
Trombetta, whose charter for teens in foster care is fighting to remain open in the face of allegations of financial and academic problems, said the issue has been resolved.
Tatkovski said PSERS announced the change to an electronic system in June 2011.