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.

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.