"The vote is a clear signal from M&S shareholders that they have serious reservations about the company's decision to ignore well-established best practice," said PIRC managing director Alan MacDougall.
So far this year, an average of only 2% of shareholders of FTSE 100 companies have opposed the re-election of its directors.
During the meeting, Sir Stuart defended his role to the company's investors, insisting that the board's "strong, independent and challenging" non-executive directors would keep him in check.
Supporting Sir Stuart, M&S deputy chairman Sir David Michels said: "He unquestionably has the right set of skills to take Marks and Spencer forward and to complete the job he has started."
In a letter to shareholders in April, M&S said appointing a new chief executive in 2008 or 2009 to replace Sir Stuart "was likely to be a damaging and unwelcome distraction at precisely the time that the business needed clear leadership to sustain its recovery and transformation".
Last week, M&S' shares fell almost 25% after Sir Stuart said that the company faced up to two years of difficult economic conditions that will hit its profits.