The father of the boy is understood to have been discovered nearby, with authorities suspecting at this stage a murder-suicide. The father, 40, was found with a gunshot wound to his head.
The three-year-old boy was discovered on Sunday morning by hunters near the village of Santa Margarida da Serra, approximately 80 miles south of the Portuguese capital.
The worried mother is thought to have reported her son missing around a week ago, when he did not return from a weekend stay with his father.
The mother has not been named, but local reports say she is a British expat residing in Lisbon.
The Judicial Police are handling the investigation.