Emergency services were called to a unit on Park Street in the coastal town of Evans Head following a concern for welfare at 8.10am.
When they arrived, police officers found the body of a 60-year-old woman in the boot of a car.
Police said a 39-year-old man, who was known to the woman, was arrested at the scene and taken to Ballina Police Station.
The man has been charged with murder (DV) and improperly interfere with corpse or human remains.
The man was refused bail and will appear at Lismore Local Court tomorrow.