Jail officials said they received a complaint by a newly-admitted inmate against Thakur for allegedly misbehaving and violating rules and regulations.
Thakur denied any wrongdoing and claimed jail officials were regularly beating him up.
Additional Session Judge Yogesh Khanna taking note of the complaints against Thakur, forwarded by the jail authorities, said: "A complaint filed by inmates of ward number 1 regarding misconduct and harassment in the prison by accused Akshay has been received."
"Application is moved on behalf of accused Akshay stating, inter alia, that he has been beaten by Mandeep Dahiya and Jitender Patel, both jail officials," the court said.
The court directed the jail authorities to medically examine Thakur and inquire into the whole matter and file a report Friday.
"It is stated by counsel for Akshay that he has been beaten on his chest. His medical examination be got done. Jail superintendent is directed to inquire into the matter and file a report by tomorrow," the court said.
Thakur is in judicial custody along with other co-accused in the gang-rape in which a 23-year-old woman was brutally tortured and gang-raped in a moving bus. She later died in a Singapore hospital.