Lakhvi's lawyer Khwaja Sultan filed the application in the Lahore High Court that alleged Lakhvi faced a threat to his life.
The application also said that authorities at Adiala Jail in Rawalpindi were not allowing Lakhvi to meet his lawyer.
Lahore High Court Chief Justice Khwaja Muhammad Sharif heard the application.
The court issued notices to the federal Interior Secretary, Attorney General and Advocate General of Punjab province to respond to Lakhvi's plea at the next hearing, which has been scheduled for Jan 21.
The Chief Justice also issued notice to the superintendent of Adiala Jail and directed him to allow Lakhvi to meet his lawyer.
Lakhvi and six other suspects were indicted by the anti-terror court for planning and helping execute the attacks that killed 166 people in India's financial hub last year.