Harner's dismissal came after Corbett, a Republican, removed Ron Tomalis in May without explanation.
An administration statement on Harner's resignation gave no reason for the move. But a Corbett spokeswoman, Lynn Lawson, said later that it involved a personnel matter that did not arise during Harner's time in the Corbett administration.
Lawson could not explain why the administration was unaware of the undisclosed personnel matter before Harner was nominated, and she could not say how or when the administration became aware of it.
"Since it is a personnel matter, I am not going to get into the specifics beyond what we've announced today," Lawson said.
Harner knows why he was dismissed, Lawson said.
Harner, 56, told an Associated Press reporter earlier Monday as he was walking into the Capitol that he knew nothing about his nomination potentially being withdrawn and that he still expected to be confirmed by the Senate next month. About 90 minutes later, the administration announced his departure.
Harner replaced Ron Tomalis on June 3 after previously serving five years as the superintendent of the Cumberland Valley School District, a large district in suburban Harrisburg. His contract with the district was ending June 30, and the board there had not approved a new contract with him before Corbett nominated him in May.
A Cumberland Valley district spokeswoman would not say whether or when the Corbett administration had sought access to Harner's personnel information on file there.
"Cumberland Valley School District considers routine employment verification requests as a personnel matter; for privacy purposes, we do not provide comment on personnel matters," spokeswoman Tracy Panzer said in a statement.
The upheaval at a major agency comes as Corbett gears up for re-election, and is inconvenient timing for a governor who is sustaining heavy criticism for cutting aid to public schools while seeking to advance the fortunes of private, parochial and charter schools.
Harner was immediately replaced as acting secretary of education by Carolyn Dumaresq, the department's executive deputy secretary who is a holdover from the administration of former Gov. Ed Rendell, a Democrat.
Dumaresq, who has a doctorate in education from the University of Pennsylvania, is a former public school teacher, superintendent, college professor, teacher's union official and president of the Pennsylvania Association of School Administrators.