The nurse was allegedly left holding the baby's torso while its decapitated head was left inside the mum's body in the reported horrific incident on January 6.
The baby's father, alleged that staff at the community health centre in Jaisalmer's Ramgarh didn't inform him about the botch-up.
"Doctors at the government hospital in Jodhpur found that the body of the baby was split into two and only the head remained, while the other half was already taken out".
The mother, who has been named by local media as "Dikhsha Kanwar" is reportedly fighting for her life in hospital following the incident.
The horrifying incident occurred on Monday at Ramgarh primary health centre (PHC) in Jaisalmer.
In June a year ago, a British gynaecologist was found guilty of medical misconduct, after she accidentally decapitated an unborn baby in the womb.
The boss of the Ramgarh community health centre claimed he wasn't around at the time of the incident.
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Later, a team of doctors headed by Dr Ravindra Sankhla operated the victim again and found that the foetus' head is in the womb.
After the incident, they asked family members to take the woman to Jaisalmer claiming that the opening of the womb had closed and it was hard to take the umbilical cord out.
The nurse, instead of treating the woman, hid the dismembered part of the baby and sent her off to another hospital, the woman said in a complaint to the police.
"We have registered a case against two staffers of Ramgarh hospital and have interrogated them", he was quoted as saying.
"When questioned, the hospital staffers handed over the lower part of the foetus to us", investigating officer Jalam Singh said in a statement.
No arrests have been made so far.