Harner, a retired Army officer turned educator, could not be reached for comment. Before his firing Monday, he was awaiting Senate confirmation.
Earlier Monday, Harner visited Cheltenham Township, where he spoke with teachers and school officials about, among other subjects, what inspired him as an educator. He made no mention of his impending resignation.
In a statement posted online Monday night by The Sentinel of Carlisle, Harner said he was proud of his accomplishments, adding: "It remains my understanding and belief that any complaints made during my tenure as superintendent were fully investigated and no matter was ever determined to be of merit or legal consequence."
Lynn Lawson, Corbett's spokeswoman, would not discuss the reason behind Harner's firing, except to say: "It is a personnel matter entirely."
Cumberland Valley School District officials also declined to talk about Harner's personnel history.
In his statement, Corbett said Carolyn Dumaresq, the department's executive deputy secretary, will serve as acting Secretary of Education, effective immediately.
Harner's resignation from the $140,000-a-year position is yet another in a string of high-profile departures from the administration - including six cabinet members in the last 15 months - even as Corbett has struggled to improve sagging poll numbers as he gears up for reelection next year.
It also has raised questions about the administration being unaware of the complaint against Harner when the governor nominated him in May. Several sources familiar with the events leading to Harner's nomination insisted Harner did not disclose the matter when he was interviewing for the position. The administration would say little Monday about its vetting of Harner.
But privately, Corbett confidantes said a second and more extensive background check is conducted once someone has been nominated to a cabinet position, and that is when the governor's office discovered the allegations,Cumberland Valley School Board had kept under wraps.
The board had even hired an outside law firm to investigate the complaint against Harner, the sources said, adding that the law firm concluded Harner had not violated any laws or district policy. Other complaints were also made, but the nature of them could not be determined Monday.
"The Corbett administration were the ones who found out about this - and they were the ones who immediately acted on it," one administration official said.
Corbett named Harner in mid-May to replace former Education Secretary Ron Tomalis. At the time, The Inquirer reported that the reasons for Tomalis' departure included behind-the-scenes tension between him and some members of the governor's inner circle.
Before joining the administration, Harner, a one-time Philadelphia School District administrator who grew up in Cheltenham, held the top job in Cumberland Valley, one of the Harrisburg area's largest districts, for nearly five years.
He has an extensive background in public school administration, and his career has had its share of controversy.
Harner ran the Greenville County, S.C., school system from 2000 until 2004, when he resigned before his contract expired. According to newspaper accounts at the time, he was criticized by school board members and others for a controversial timber sale, in which he raised money to start a lacrosse program by selling trees from lots being cleared for district construction projects. He also clashed with parents over changes in school schedules.
He was credited with a number of successes in the South Carolina district, including raising students' test scores.
Harner went on to the Gainesville, Ga., school district, and then to Philadelphia, where he was a special assistant to former city School Superintendent Paul Vallas and later a regional superintendent.
In 2007, the Toledo, Ohio, school board chose Harner to lead the district. The Toledo Blade reported that he withdrew from contract talks after some board members objected to his proposal to live outside the district and send his daughter to private school. The newspaper said e-mails showed Harner's lawyer had asked about whether the district would pay the daughter's tuition. Harner said he had never wanted the district to pay her tuition.
Contact Angela Couloumbis at 717-787-5934 or firstname.lastname@example.org, or follow on Twitter @AngelasInk.
Inquirer staff writers Amy Worden and Daniel Rubin contributed to this article.