The mum was apparently so concerned that it would disadvantage the boy when he got older that she drowned him in the bath.
Police in the Indonesian capital Jakarta said the 38-year-old woman 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.
The woman is not thought to have been charged but is believed to be in custody.