Sadhvi had moved the application last month on the ground that she was suffering from breast cancer.
However, special NIA prosecutor Avinash Rasal argued that she was getting proper medical treatment at government hospitals while in judicial custody.
She owned the motorcycle used to plant the bomb and there was no evidence that it had been sold to anyone else at the time of the crime, he said.
Recently, the court also rejected the bail pleas of Lt Col Prasad Purohit, Dyanand Pandey alias Swami Amritanand Dev, Rakesh Dhawade and Major (retd) Ramesh Upadhyay, all co-accused in the case.
Twelve persons, including Sadhvi Pragya Singh Thakur and Purohit, were arrested for carrying out a blast at Malegaon, a predominantly Muslim town in north Maharashtra, on September 29, 2008, killing six persons and injuring 100 others.
The accused have been booked under stringent MCOCA, Unlawful Activities Prevention Act and IPC.
Following a Supreme Court order, a special court has been constituted to exclusively hear the case.
Sadhvi is also an accused in the case related to the murder of Rashtriya Swayamsevak Sangh activist Sunil Joshi in Madhya Pradesh.