US Edition Dr. Luiz Cesar Soltoski told The Associated Press that surgeons hope to remove most of the needles – some as long as 2 inches – but because some are stuck in his lungs, they have to wait until the child's breathing improves.
Some cannot be removed; they are too close to vital organs or actually inside them, Dr Soltoski said.
The boy's mother, a maid, brought him to a hospital in the small north-eastern city of Ibotirama on Thursday, saying he was complaining of pain. Three days later, after X-rays revealed some of the needles, doctors transferred the little boy to a larger hospital in Barreiras.
The mother told police she did not know how the needles got inside her son, but police said they were seeking the boy's stepfather.
The local police chief, Helder Fernandes Santana, told reporters that the man had disappeared on Tuesday, as police questioned the boy's relatives in what was being treated as an attempted homicide.
The boy's name was withheld because of his age.
Dr Soltoski said he believed the needles were stuck into the toddler's body one by one because it would have been impossible for him to swallow them.
"We think it could have only been by penetration because we found needles in the lung, the left leg and in different parts of the thorax. It couldn't have been by ingestion," Dr Soltoski said.
Doctors found no signs of outside wounds on the boy, but X-ray images carried by Brazilian websites clearly showed some of the needles inside his body.
The boy is in intensive care, but Dr Soltoski said his condition had improved since he was admitted.