The University of Virginia’s accrediting body has placed the elite public flagship “on warning” for allegedly violating two compliance standards when members of the school’s governing board covertly planned an ouster of President Teresa A. Sullivan, privately asking her to resign in early June and then unanimously reinstating her 18 days later.

The Southern Association of Colleges and Schools Commission on Colleges, which accredits schools in 11 states in the South, had accused the U-Va. Board of Visitors of compromising the university’s integrity, not having a formal policy for involving faculty in making decisions and not following its governance requirements, which forbid a small number of members from controlling the board.

On Tuesday, commission trustees announced that they determined that the university was not in compliance in two of the three areas: those concerning faculty involvement and following governance requirements.

The U-Va. board has repeatedly denied the allegations. In written correspondence with the commission this fall, board leaders maintained that although mistakes were made during the failed ouster — which threw the historic Charlottesville campus into turmoil — the board never violated accreditation standards, state laws or its own policies.

The commission has placed the university on warning for one year and will send a team to Charlottesville early next year to investigate further, according to an e-mail U-Va. Provost John D. Simon sent to the school community Tuesday afternoon. Simon is handling the inquiry; Sullivan has recused herself from the process.

In an exclusive interview with The Washington Post, University of Virginia President Teresa A. Sullivan speaks out about her ousting by the university’s Board of Visitors in June, the tumult that followed and her eventual reinstatement. (Brad Horn, Donna St. George, Jenna Johnson/The Washington Post)

“This action does not imply any criticism of the University’s academic quality and programs, nor does it affect the institution’s ability to receive federal aid, including financial aid and sponsored research,” Simon wrote, adding that the university “pledges to work diligently to address the concerns cited by the commission.”

A warning is one of the commission’s lesser sanctions, though it could lead to a school later facing probation, according to a policy posted on the commission’s Web site. The longest a school can remain on warning is two years. Accreditation is required for universities to receive federal funding, and concerns about a school’s standing can hurt its reputation.

Belle S. Wheelan, president of the commission, has said that it would be “very unusual” for U-Va. to lose its accreditation. She described such a warning as “a black mark on an institution,” but said Tuesday that she expects U-Va. to address the commission’s findings.

“I have every faith that they will do everything they need to do in the next 12 months to come into compliance,” Wheelan said.

It has been six months since the university’s leadership crisis, but questions remain about what exactly happened, the specific reasons Sullivan was asked to resign and what changes occurred to motivate the board to unanimously reinstate her. In early November, the U-Va. board voted to extend Sullivan’s contract for another year, through July 2016.

The leader of the board, Rector Helen Dragas, has remained in her position despite hundreds of calls from faculty, alumni and others for her resignation. Soon after Sullivan was reinstated, Gov. Robert F. McDonnell (R) reappointed Dragas to the board for another term.

The U-Va. board has also enacted changes aimed at preventing its repeating missteps that occurred in June. The board’s manual now requires that appointment, “removal, requested resignation, or amendment of the contract or terms of employment of the President may be accomplished only by vote of a majority (or, by statute, two-thirds in the case of removal) of the whole number of Visitors at a regular meeting, or special meeting called for this purpose.” The board also plans to institute quarterly evaluations of the president and to better involve faculty members.