Five suburban districts and one local charter school outside Philadelphia were named in the report and will also be asked by the state to investigate the 2009 results.
The Bristol Borough school system had one school, Snyder-Girotti, where two grades had multiple flags. Cheltenham, Strath Haven, Pennsbury, and Spring-Ford High Schools all had multiple flags for their 11th grade tests. Chester Community Charter School was flagged for four grades.
Though the report was finished in July 2009, it languished for two years until the Philadelphia Public School Notebook began asking questions about it recently.
Tomalis said he first read the report this week.
"Reading it, there are some red flags," Tomalis said. "And it really didn't see the light of day in 2009. It was lost, buried. Some of the indications are that there are things we certainly need to follow up on."
He said the department had begun a probe of why the report disappeared.
Test security was a key issue for him even before questions were raised about the 2009 PSSA scores.
After he was named Gov. Corbett's secretary of education in January, Tomalis said, he began asking questions about what kind of extra security the state had in place to analyze tests.
"I was told there was none," he said.
The state spent $108,000 on the 2009 forensic analysis, but that was cut from the 2010 budget. Tomalis had earlier ordered the report to be reinstated for the most recent Pennsylvania System of School Assessment (PSSA) exams.
"That amount of money is a very, very good investment," he said.
Now, Tomalis said, he's asked for the results to be analyzed for 2010 as well.
"That way, we won't just get one snapshot," he said. "If there are trends that are disturbing, we will continue to act aggressively."
He expects the 2010 and 2011 reports to be completed by early fall.
For now, the department has told 40 districts and nine charter schools statewide to investigate irregularities flagged on their 2009 PSSAs.
They must report back to the Department of Education within 30 days.
"That will just be the first look. We will then see what the individual school district's response is," Tomalis said. "That will not be the last look. If necessary, we will further pursue the issue and take all necessary action."
Tomalis declined to say what that might be.
Among the schools flagged in the 2009 report is Roosevelt Middle School. As The Inquirer reported in May, multiple Roosevelt teachers said they witnessed many test security breaches, and they attributed a remarkable two-year rise in state test scores to cheating.
The district this spring conducted its own investigation into Roosevelt testing improprieties and found claims of cheating unfounded.
Roosevelt was flagged by the state for both reading and math irregularities for both grades that attend the school.
The secretary said he was aware of the claims.
"I am indeed looking at issues that have been raised in the Philadelphia School District. I'm awaiting the report that will come from Philadelphia. In certain circumstances, it does lead me to look harder as to what might be happening with the PSSA," Tomalis said.
Philadelphia district officials have defended their test security and the integrity of their employees, promising to reopen old investigations and launch new ones.
Contact staff writer Kristen Graham at 215-854-5146, email@example.com or on Twitter @newskag. Read her blog, "Philly School Files," at www.philly.com/schoolfiles.
Inquirer staff writer Larry King contributed to this article.