He said although the injuries were not accidental, the Crown could not prove the circumstances they were inflicted in.
The court heard it was during a visit to a Hastings GP in April 2011 for an immunisation that the doctor noticed an issue with the baby boy's thigh.
The baby was taken to the Hawke's Bay Hospital where X-rays were taken.
A fracture to the thigh bone was found, as well as fractures to the lower legs, pelvis, toe and rib.
A paediatric radiologist from Auckland gave evidence that the injuries would have been painful for the baby and that at least two of them would have required significant force to inflict.
In relation to a fracture found on the upper thigh, the doctor said the baby would have been in a great deal of pain.
"It would have been a direct blow to the bone, a significant blow. We sometimes see these where a parent has accidentally fallen on a child," the radiologist said.
Mr Manning asked how the fractures would have affected the baby when he was being held or bathed.
"If you transposed any of these fractures on to one of us, as adults, we would all know we've got them. It's that femur one, that is almost completely displaced, for you and I, that would be excruciating. Any movement of that leg would exacerbate that so the child would have been very unhappy."
Another paediatrician, who treated the baby at the Hawke's Bay Hospital, agreed the femur fracture would have been the most painful.
"A baby, who sustained a fracture of the upper part of the thigh bone, would be in immediate and obvious pain.
"You're going to have a baby screaming ... "
He said the injury would be "obvious and distressing" to an adult in charge of the care of the injured baby.
The doctor said he had not been able to gain a satisfactory explanation for the injuries from the baby's parents.
"I didn't receive any explanation that explained the extent of the trauma that was obviously there."
He said there were no outward signs of any of the fractures apart from swelling.
The trial continues today.