"The investigator has given him no permission," the source said citing no reasons for the refusal.
Emelianenko asked the chief of Moscow's Butyrka prison to register his marriage on October 27.
According to investigators, Emelianenko, 33, raped his housekeeper in March and stole her passport. He was detained in May in the southern Russian city of Tambov where he got into a car accident.
In August 2013, another woman accused Emelianenko of rape but later withdrew her accusations.