The 40-year-old doctor, an orthopedic surgeon who has not been named, was taking his son to nursery in the southern coastal town of Larnaca when he received an emergency call at around 8am on Tuesday
He drove to a private clinic and left the boy in the car, police said.
It was only when his wife called him more than eight hours later, after she had gone to collect the child from his nursery, which the father realised what he had done.
He found his son unconscious in the back seat of the car, with an empty water bottle beside him.
Colleagues from the clinic were unable to revive the boy.
A post mortem carried out on Wednesday indicated that the boy could have died from a heart attack.
"The child had quite serious heart problems that were discovered during the autopsy. For a final conclusion we must await the results of tissue tests," said pathologist Eleni Antoniou.
"Small children can withstand high temperatures for many hours. The possibility of death by heatstroke or asphyxiation is excluded here." The car in which he was found was towed away and impounded by the authorities.
Temperatures in Cyprus have reached 117F (30C) this week.
A Korean couple let their baby starve to death while they were busy raising a virtual child online, police said.
The couple, from Suwon in South Korea, would leave their three-month-old daughter home alone in their apartment while they spent up to 12 hours a day playing a Second-Life style3D fantasy game called Prius Online, The Sun newspaper reports.
Police said the couple had become totally immersed in the online game and neglected their real lives, giving their daughter just a bottle of milk per day.
Father Kim Yoo-chul, 41, and 25-year-old mother Choi Mi-sun called paramedics when they arrived home from a stint in a net cafe to find their daughter dead In September last year.
The couple first told police they had found their daughter dead when they woke in the morning, but suspicions were raised by the malnourished state the baby was found in.
"She appears to have starved to death because she was not fed for such a long period of time," a spokesman for Korea's national crime laboratory said after an autopsy was carried out.
The couple fled after the baby's funeral, but police tracked them down and charged them with child abuse and neglect on Tuesday.
The parents told police they had not been to a net cafe in their five months on the run due to their "sense of guilt".
South Korea, one of the most wired countries in the world, has a high rate of internet game participation among its population