The Australian singer and the French actor confirmed the split in a statement released late Friday.
"They have made it clear that the decision to go their separate ways was mutual and amicable," the statement said, adding that the two remain close friends.
Minogue recently resumed performing after treatment for breast cancer, diagnosed in 2005.
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In November, Minogue, 38, told Elle magazine that Martinez had been an "incredible" support during her illness.
"Olli was there all the time, helping with the practical stuff and being protective," she was quoted as saying. "I don't like to say too much in public about Olivier, as he's a very private person, but I will say that he was incredible."
Recently, Britain's tabloid media has speculated that Martinez was seeing someone else.
In the statement, the couple said that "the media's false accusations of disloyalty have saddened them both."
Minogue recently completed her Showgirl Homecoming tour, although she was forced to cancel two concerts last month because of a respiratory tract infection.