Scottish Public Services Ombudsman Jim Martin also said staff at the GP practice should offer to meet the parents to "re-enforce this apology".
He launched an investigation after the boy's mother, identified as Mrs C, complained about the care her child received.
Mr Martin ruled the practice had failed to provide the boy with "appropriate clinical treatment" and had "unreasonably delayed" referring him to hospital.
The Ombudsman's report told how the boy, then aged six-and-a-half, attended the GP surgery several times between May 2011 and September 2011, complaining of weight loss, fatigue, vomiting, nausea and bone pain. He was seen by a number of doctors there and various examinations and tests were carried out. When his condition did not improve, he went to Ninewells Hospital in Dundee and then the Royal Hospital for Sick Children in Edinburgh, and was diagnosed with stage four Burkitt's lymphoma - a form of non-Hodgkin lymphoma. Despite treatment, the youngster died in May 2012.
The report said: "It is clear Master A attended the practice several times with the same problems, Mrs C expressed repeated concerns about his condition, the symptoms Master A was experiencing were in the list of possible symptoms of cancer and his health was not improving."