The document was filed in the court of Special Judge.
Besides Pragya, who is under judicial custody, the other accused include Rajendra Choudhary, Lokesh Sharma, Jitendra Sharma, NIA said in a press release.
"The charge sheet also cites supplementary evidence against Pragya Singh Kushwaha for her role in the crime, since she has been charged earlier in the charge sheet by Madhya Pradesh police in 2011", it said.
Joshi was shot dead on December 29, 2007 near Dewas, about 150km from here.
Pragya, who is ailing and undergoing treatment at a city hospital, is also an accused in the 2008 Malegaon blast case.
According to NIA, Rajendra and Lokesh had fired at Joshi. Jitendra had arranged the murder weapon (pistol) and given it to Balbir.