Hyderabad Lok Sabha member Owaisi alleged on a micro-blogging site that most of the witnesses in the Mecca Masjid blast case had turned hostile after June 2014 and the NIA either didn't pursue the case as was expected from it or was not allowed by its political masters to do so.
Asserting that "justice hasn't been done in the case," Mr Owaisi said "questions would be raised over the criminal justice system (of the country) if such biased prosecutions continue."
The firebrand MP alleged that the Modi government did not even appeal against the bail given to the accused earlier.
"Justice has not been done, the NIA & the Modi govt didn't even appeal against the bail that was given to the accused within 90 days. This was a complete biased investigation which will weaken our resolve to fight terrorism," said Mr Owaisi, recaling that nine persons had died and many more were injured in the 2007 blast.
A special NIA court in Hyderabad acquitted five persons on Monday, including Swami Aseemanand, in the case. Nine persons had been killed and 58 injured in the blast.
The five who faced trial included Devendra Gupta, Lokesh Sharma, Swami Aseemanand alias Naba Kumar Sarkar, Bharat Mohan Lal Rateshwar alias Bharat Bhai and Rajendra Choudhary.
Two other accused in the case, Sandeep V Dange and Ramchandra Kalsangra are still absconding, while another accused Sunil Joshi had died.
The NISA is still probing the case against the two absconding remaining accused.