The Bombay High Court said the 2006 Malegaon blasts case “seems to have reached a dead end” while discharging four accused, sharply criticising the NIA for completely ignoring crucial evidence earlier collected by the Anti-Terrorism Squad (ATS) during its initial probe.
The Bombay High Court said the 2006 Malegaon blasts case seems to have reached a dead end, while discharging four accused and criticising the NIA for completely ignoring evidence gathered by the earlier Anti-Terrorism Squad (ATS) probe.
The court’s order also left unresolved who was responsible for the explosions that killed 31 people.
The High Court discharged the four accused Rajendra Chaudhary, Dhan Singh, Manohar Ram Singh Narwaria, and Lokesh Sharma observing that there was not enough evidence to put them on trial.
They had been charged under sections of the Indian Penal Code related to murder and criminal conspiracy, as well as under the Unlawful (Activities) Prevention Act (UAPA), which is widely viewed as a stringent anti-terror law.
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While quashing the September 2025 special court order that framed charges against the four accused, the High Court noted that the judge at the time had not “applied his mind”.
Earlier, On September 8, 2006, four bombs detonated in Malegaon town in Maharashtra’s Nashik district. Three explosions occurred inside the premises of Hamidia Masjid and Bada Kabrastan shortly after Friday prayers, and the fourth took place at Mushawarat Chowk, killing 31 people and injuring 312 others.
In its judgment delivered by a bench of Chief Justice Shree Chandrashekhar and Justice Shyam Chandak, the High Court stated that the National Investigation Agency (NIA) “completely ignored” both the ATS probe and chargesheet, which the court said provided a detailed account of the planning by nine Muslim men arrested earlier in the case.
The investigation, the court noted, saw several twists and turns. Initial agencies had claimed the conspiracy was hatched by the Muslim accused, but the NIA later alleged that right-wing extremists were behind the blasts.
The HC order said,
“The case seems to have reached a dead end. The diagonally opposite stories in the chargesheet filed by the ATS and the NIA lead nowhere,”
The court observed that the ATS had collected incriminating evidence from the incident site, and that forensic findings indicated traces of RDX in soil samples taken from the place of occurrence and from the godown of one of the nine accused. It added that both samples were “found to be the same”.
The High Court further said that when framing charges for a grave offence such as murder offences that may lead to the death penalty the trial court must ensure there is sufficient material to proceed against the accused.
It said,
“The special judge overlooked the inherent contradiction and intrinsic improbability in the prosecution story as put forth by the NIA,”
The court also stated there was no explanation for how the evidence collected by the ATS and the CBI could be set aside by the special court. It said the prosecution’s case now presented “two contradictory versions” and that the accounts filed by the ATS and the NIA could not be reconciled.
The High Court held that the earlier evidence gathered by the previous probing agencies was not wiped out and therefore still had to be considered by the special court. It also noted that at the charge-framing stage, the trial court has the power to sift and weigh evidence only to determine whether a case is made out against the accused.
The court said the prosecution’s case against the four accused rests only on circumstantial evidence. It added that no one had testified that they saw the accused participate in the bomb blasts, and that the NIA had largely relied on confessional statements that were later retracted, along with statements made in another case.
It said,
“This is a mystery why the NIA did not collect fresh materials,”
The court also pointed out that the NIA, after its investigation, adopted a different narrative based on the statement of Swami Aseemanand, who later retracted it.
The HC said,
“The NIA has projected an entirely different story and states that the investigation of the case is still continuing and further evidence is being collected against the accused persons, and had requested the special court to permit it to continue further investigation of the case,”
The High Court further said that the materials relied upon by the NIA to show the appellants purchased bicycles used in the crime were based on hearsay.
It also noted that in its chargesheet, the NIA named four persons as wanted accused, two of whom had later also been shown as wanted accused in the September 2008 Malegaon blast.
Former BJP MP Sadhvi Pragya Singh Thakur, then Lt Col Prasad Purohit and five others were arrested and faced trial over the alleged role in the 2006 blast. Last year, in July, a special court acquitted all seven accused citing a lack of evidence.
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In the NIA’s chargesheet for the 2006 case, the agency relied on a statement attributed to Swami Aseemanand, which said the Malegaon blasts were carried out by associates of the deceased right-wing activist Sunil Joshi. After Aseemanand retracted the statement, the NIA filed a chargesheet giving a clean chit to the nine Muslim accused and naming the four present appellants.
Earlier, in 2016, a special court discharged the nine Muslim men, an order the ATS challenged in the High Court. That appeal is still pending and has not been heard since 2019.
The High Court, in 2019, granted bail to the four accused, noting that they had spent more than six years in custody without trial.