A request to illuminate the 2,500-year-old Parthenon with red floodlights to mark World AIDS Day on Dec. 1 was turned down.
The ministry's powerful Central Archaeological Council ruled that the idea floated by the Health Ministry would cause an unwelcome "alteration" to the all-marble building - Athens' most famous landmark.
"The Parthenon is already floodlit (at night) in a specific way that shows it to its advantage," senior ministry archaeologist Eleni Korka said.
"Council members agreed that something of the sort would constitute an alteration, and for a monument like that it would not be fitting," added Korka, head of the ministry's directorate of prehistoric and classical antiquities.
While faded to a well-weathered white now, much of the Parthenon was initially painted in bright colors during ancient times.
Government officials are highly protective of the Acropolis temples, seen as the crowning achievement of ancient Greek culture.