The 37-year-old had been in a coma since last Tuesday at a hospital in Poland - where he was participating in the world championship - after collapsing and being found unconscious in his hotel room.
Kiligkaridis, a father of two, had not shown any signs of health problems and a few days before the world championship he had undergone routine medical tests that had shown nothing of concern.
"The federation mourns the loss of Andreas Kiligkaridis, his passing has made Greek canoeing poorer," said the Hellenic Canoe-Kayak Federation in a media statement.
"In his race for life unfortunately he did not win, breathing his last breath in a hospital in Poland after a brave battle. The federation shares the pain of his family and our thoughts are with them. Have a safe journey Andreas."
Kiligaridis, a flatwater sprint canoe specialist, competed for Greece in three Olympic Games in 2000, 2004 and 2008.