Ten persons belonging to right-wing organisations were named as accused in the case, but only the five arrested had faced trial.
Sandeep V Dange and Ramchandra Kalsangra, who were also accused in the incident, are absconding.
Investigations against two others from the same State, Tejram Parmar and Amith Chowhan, are continuing.
He criticised the NIA and said that the verdict given today weakens India's resolve to fight terrorism. Speaking to CNN-News18, former home minister, Shivraj Patil refused to apologise.
BJP does not comment on the judgement of the court.
A lawyer of one of the accused told reporters outside the Nampally criminal court complex here that the court held that the prosecution failed to prove the charges.
"People who perpetrated the attack were protected through misuse of agency (NIA). Will Congress or anyone else who propagated this theory compensate them?" In a series of tweets, Owaisi said that the NIA team did not "pursue the case as expected". He further said that he never used the word Hindu terror. The Five others were killed in police firing. There was no admissible evidence against them. The court, however, would deliver its verdict for only five accused. "It is disappointing. It reflects on the efficiency of the country's premier anti-terror Investigation agency", said noted human rights activist MA Shakeel.
The Hyderabad-based court set them free over lack of evidence. A total of 58 persons were injured.
Last week, the court had posted April 16 as the date for pronouncing the judgement in the case.
March 31, 2017: Aseemanad was acquitted in the Ajmer Dargah bomb blast case.