Accepting his request, the court directed the jail authorities to keep Amarchand separately from the other accused in the case and have sent him to judicial custody till Jan 3.
Apart from Amarchand, Shahbuddin, Sohan Ram and Baldev are the ones who are accused in the conspiracy to abduct Bhanwari Devi.
"He is fearing threat to his life in the jail. He might be subjected to threats or manhandling from these accused," said Manish Vyas, Amarchand's counsel.
CBI also said that there were possibilities that Amarchand could be persecuted by the accused in jail, forcing him to change his statements.
Amarchand had earlier confessed to playing a part in the conspiracy to kidnap his own wife.
Bhanwari Devi, an auxiliary nurse went missing from Bilara, Rajasthan on Sept 1 and has not yet been found.
Earlier, reports had revealed that the nurse could have been killed. There were also claims that the 36-year-old nurse could have been killed on Sept 1 itself, the day she was abducted.
According to a source, Sohan Lal, a prime accused in the case used his mobile to click pictures of the nurse's body.
It is yet to be ascertained if the nurse has been killed as she still remains untraceable.