The percentage of Pennsylvania students meeting state math and reading standards on the PSSAs - the annual academic accountability test - declined this year for the first time since the tests began in 2002.

Education Secretary Ron Tomalis on Friday attributed the drop to tight security procedures enforced during the spring testing, especially in 110 schools across the state still under investigation for possible cheating from 2009 to 2011.

This is the first year, Tomalis said, that the public can be confident that, overall, test scores are not tainted by adult interference. "We have hit the reset button on student performance," and the 2012 scores provide a new baseline, he said.

Well over 100 educators will eventually face state disciplinary charges for cheating that could lead to the revocation of their professional certificates, Tomalis said. But that could take years, and the results of state disciplinary board hearings in Harrisburg would be disclosed only if educators were disciplined.

In Philadelphia, 53 district-run schools and three charter schools are still under investigation for allegations of cheating in past years.

Of those 53, all but two experienced declines in both subjects from the previous year. The Philadelphia Military Academy at Elverson had a 71 percent decline in math scores from 2011 to 2012, the biggest drop of any city school. The two other schools had a decline in either math or reading.

Statewide, the 110 schools that had been under investigation this year for cheating averaged a double-digit drop in math and reading scores. With those schools taken out of the mix, math and reading scores for students statewide would have declined about 0.5 percent. With the investigated schools included, they were down about 1.5 percent.

Last year, 77.1 percent of the state's students scored at or above grade level on the math test; this year, 75.7 percent met the mark. In reading, student scores declined from 73.5 percent at grade level to 71.9 percent. Tomalis called those percentages "unacceptable for Pennsylvania," adding that everyone needs "to redouble our efforts."

In Philadelphia this year, 50 percent of students districtwide performed at grade level in math, 45 percent in reading. That is down from 59 percent in math and 52 percent in reading last year.

"These results are clearly disappointing, and they simply remind us of the work we have ahead in developing a strong system of schools in Philadelphia and in supporting our students' learning," School Superintendent William R. Hite Jr. said.

The news was not all bad. The High School of the Future was one of the most improved schools in the district. It rose 27.2 percentage points in reading and 22.8 percentage points in math.

"I took a double take," said longtime district principal Rosalind Chivis, who has been at the helm of the 425-student school since 2008. "I knew we would improve, but it blew me away when I saw the data. I was so very proud of the learners. They worked really, really hard, and a big part of it is motivating them to do well, to take the test seriously and do well."

Along with the decline in test scores, the number of schools statewide meeting achievement benchmarks declined sharply from last year, in large part because Pennsylvania's No Child Left Behind school accountability standards went up a sizable amount from 2011.

The state thresholds went up from 67 percent of students required to make the mark in 2011 to 78 percent this year. In reading, the benchmark went from 72 percent to 81 percent.

This year, 51 percent of schools statewide met state academic benchmarks by having the required percentage of students scoring at grade level or above. That was down from 75 percent in 2011.

In Philadelphia, only 33 - 13 percent - of the district's 250 schools met state standards, down from 41 percent in 2011.

Among city charter schools, 54 percent met the benchmarks, down from 63 percent in 2011. In Philadelphia's suburbs, 65 percent of schools made the mark, down from 81 percent.

Statewide, in addition to Philadelphia, five districts and three charter schools remain under investigation for cheating from 2009 to 2011, Tomalis said. They are the Harrisburg, Hazleton Area, Pittsburgh, Reading, and Scranton districts and the Imhotep Institute, Philadelphia Electrical and Technical, and Walter D. Palmer Leadership Learning Partnership charter schools.

An additional five districts and one charter school that were under investigation this year will continue to be monitored and will have strict new test security measures. Though no one was identified as having cheated, there was no satisfactory explanation of the irregularities at those schools, Tomalis said.

Some educators and education advocates blamed the drop in student performance on reduced funding for schools.

"It defies logic that they could expect student performance to improve after cutting nearly $1 billion" in funding in 2010-11, said Wythe Keever, a spokesman for the Pennsylvania State Education Association, the state's largest teachers' union.

Keever said cheating "is wrong. . . . Those individuals should be held accountable." But he said Tomalis was using cheating revelations to "shift attention away from the real issue: adequately funding public education."

Tomalis said the state's Technical Advisory Committee found heightened test security the only factor in the drop. "I don't buy the excuse the numbers went down because of budget cuts," he said.

Union leaders were quick to criticize state officials for tying cheating to the statewide drop in test scores.

"Any cheating on tests is deplorable, but to use an incomplete investigation involving a handful of schools and educators statewide to discredit our public schools and the educators who have dedicated their careers to helping all children reach their full potential is nothing short of a political cheap shot," Ted Kirsch, president of the American Federation of Teachers Pennsylvania, said in a statement.

Jerry Jordan, president of the Philadelphia Federation of Teachers, agreed. Cheating may have occurred, he said, but its impact is negligible.

"When resources are pulled from our schools, scores drop," Jordan said.

By 2014, according to the federal No Child Left Behind law under which the state tests are mandated, 100 percent of students should be scoring proficient or advanced. Virtually all educators see that as unrealistic.

Last year, the Obama administration started allowing states to scrap the 2014 deadline if they would agree to adopt new rules that focus on the bottom 15 percent of schools, and make other changes.

Thirty-two states, including New Jersey, and the District of Columbia have been granted the waivers.

Tomalis on Friday called it likely that Congress will pass a new version of No Child Left Behind in the next year or two and that the state did not want to keep changing accountability plans. He instead asked for federal permission to freeze test benchmarks for schools at 2012 levels, but was turned down.

Pennsylvania's academic thresholds are set to increase to 89 percent in math and 91 percent in reading next year.

Inquirer staff writer Susan Snyder contributed to this article.