Police in the capital Jakarta said today that the woman, 38, told them her son had a small penis before he was circumcised but that it was even smaller after the operation.
Spokesman Rikwanto said the mother believed the boy would have a ‘bleak future’ because of the size of his genitalia.
The woman drowned the youngster in a bath filled with water before dressing him and laying his body on a bed.
Officers said the woman is fully conscious of what she had done and had handed herself in.
But the police have also ordered her to undergo psychological tests to assess her mental state.
Rikwanto told AFP: ‘She told police investigators that she killed him as he would have a bleak future with his small penis.