A division bench headed by Justice Rajiv Shakdher passed the order on a habeas corpus plea moved by Basha's daughter Mubeena.
Basha was arrested in 1991 by the Coimbatore city police in connection with a murder case and was remanded to judicial custody.
The trial court awarded life imprisonment to him in the case.
He was also arrested in connection with the 1998 serial bomb blasts cases.
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Basha's daughter, in her plea, sought the benefit of Section 428 of the CrPC for setting off the period of incarceration already served by her father in the 1991 murder case against the jail term served in the blast case.
She contended that the sentences were ordered to run concurrently with the previous conviction in which her father was given life term.
She also referred to a 1994 scheme of the Tamil Nadu government for premature release of life convicts on humanitarian grounds after 20 years of actual imprisonment.