Reports this week said Thompson, who oversees all store operations including food, had been in talks with headhunters after becoming frustrated at a lack of responsibilities and recognition.
However, a spokeswoman said: "Anthony Thompson remains our retail director and is a much-valued member of the M&S senior team."
Even so, she admitted his departure could not be entirely ruled out. Thompson's career began with M&S in 1984. He also sits on the executive committee, which operates below board level.