The numbers didn't look right to Linda Clautti, chief executive officer of Northside Urban Pathways Charter School.

Walter Spudic, school finance director, had his own suspicions.

Their detective work showed that the Pittsburgh Public Schools had been under-funding Northside Urban Pathways and other charter schools since 1998. Shown the evidence, the financially troubled school district last fall began sending $2.9 million in makeup payments to 12 charter schools and nine cyber-charter schools.

The district sent Ms. Clautti's school two checks, totaling about $400,000.

"We've not gotten interest on any of the money," she said.

The funding mishap has become another point of contention between the school district and the charter schools that are sometimes criticized for luring away the former's students and money.

Salvador Wilcox, executive director of Education Innovations Inc., cited the funding issue this week in a letter he sent to the state education secretary requesting an investigation of the district's treatment of charter schools. The city school board Wednesday voted down three proposed charter schools, including one planned by Education Innovations.

Mr. Wilcox said the district has a pattern of thwarting competition.

School district Chief of Staff Lisa Fischetti said Mr. Wilcox's letter was timed to bring attention to the vote on his charter proposal.

Charter schools are independent public schools, paid by the school districts whose children they educate. The Pittsburgh district pays to send students to six charter schools operating in the city, to charter schools in other municipalities and to cyber-charter schools.

While he didn't rule out the possibility, state Department of Education spokesman Mike Storm said he wasn't aware of another case in which a school district routinely had shorted charter schools on monthly payments.

Some charter schools said they're going to take another look at their records to make sure the Pittsburgh district has accounted for the mistake in full. Some also said they would check to see whether they've been receiving proper payments from other school districts.

The state has a formula for determining a district's per-pupil payment to charter schools. Ms. Clautti said she and Mr. Spudic believed payments from the Pittsburgh district were too low, and discovered that district officials had applied the formula incorrectly.

After the school called the problem to the district's attention, "it was difficult to get movement" toward a resolution, Ms. Clautti said. That changed, she added, after the school called in an attorney.

Ms. Fischetti said the district moved promptly with the makeup payments after the education department concurred with Northside Urban Pathways' findings.

The catchup payments were charged to the district's 2006 budget, with some checks sent as recently as last month.

"From our standpoint, we don't feel like there was anything that was done on purpose," Ms. Fischetti said.

Still, Ms. Clautti said the issue reinforced charter schools' belief that school districts can mistreat them with impunity.

"If the situation were reversed, we would be looked upon as doing something grossly illegal and probably taken to court and shut down and everything else," she said.

Other schools were grateful that Ms. Clautti and Mr. Spudic acted on their suspicions. Makeup payments include about $482,000 to Career Connections Charter High School, Lawrenceville; about $200,000 to Manchester Academic Charter School; about $500,000 to City Charter High School, Downtown; and about $239,000 to Urban League of Pittsburgh Charter School.

"It's a windfall because it helps us provide more education, more resources, to our kids," said Richard Wertheimer, co-founder and education manager of City Charter High.