Rights groups and critics have long accused Greek police of detaining immigrants and other prisoners in shocking conditions.
Photos published in the Greek media of the men, who were aged between 20 and 25 and arrested on Friday, show them bruised and bleeding while being escorted by police.
But mug shots released by the police over the weekend had injuries missing. One had been altered to remove a purple bruise from beneath the suspect's left eye. In another, black bruises below the suspect's eyes and cheeks appear to have been erased.
Public Order Minister Nikos Dendias acknowledged the photographs had been altered, but defended the decision by saying it was to make the four men recognizable to the public.