Mumbai, April 22: After nearly two decades and investigations by three separate agencies, the question of who carried out the 2006 Malegaon blasts – which killed 31 people – remains unanswered. This comes after two different sets of accused have now been discharged by the courts.
The probe was initially conducted by the Anti-Terrorism Squad (ATS), later transferred to the Central Bureau of Investigation (CBI), and finally handed over to the National Investigation Agency (NIA).
On Wednesday, the Bombay High Court discharged four individuals – Lokesh Sharma, Dhan Singh, Manohar Singh, and Rajendra Choudhary. The court allowed the appeals filed by the four men, challenging the charges framed against them by the special NIA court on September 30, 2025. This marks the second group of accused to be cleared in this case.
The verdict follows less than a year after a special NIA court acquitted all seven accused in the separate 2008 Malegaon blast case, including former BJP MP Sadhvi Pragya Singh Thakur and Lt Col Prasad Purohit, citing insufficient evidence.
The 2006 Incident and Initial Arrests
The 2006 blasts in Malegaon, a textile town in the Nashik district, occurred on September 8, leaving 31 people dead and over 100 injured. Four bombs exploded near the Hamidia Mosque and the Bade Kabristan area during Friday prayers. A few days later, on September 13, a “fake” bomb was recovered from the staircase of the Mohammedia Mosque.
Initially, the investigation was handled by the local police before being transferred to the ATS in October 2006. The ATS arrested nine Muslim men, claiming that members of the banned group SIMI were behind the attack. Those arrested included – Noorul Huda, Raees Ahmed, Salman Farsi, Farogh Magdumi, Shaikh Mohammed Ali, Asif Khan, Mohammed Zahid and Abrar Ahmed (who later turned approver).
Two of the men, Ali and Asif, were also booked by the ATS in connection with the July 11, 2006, Mumbai serial train blasts. However, they were acquitted by the Bombay High Court in the train blasts case in July 2025. The court criticized the ATS probe, labeling the confessions as "inadmissible and untruthful" and accepting that the men had been subjected to torture.
In the 2006 Malegaon case, the ATS similarly claimed that seven of the nine men had provided confessions. These nine men remained incarcerated for six years. The CBI later took over the case, supporting the ATS's findings and adding more names, bringing the total number of accused to 13.
The Shift in Investigation
In 2010, following the 2007 Mecca Masjid blast probe, the CBI arrested Swami Aseemanand. He reportedly told a court that the 2006 Malegaon blasts were actually carried out by a Hindu extremist group.
In 2011, the probe was transferred to the NIA, which shifted the narrative. It named Sunil Joshi – a key accused in the 2008 Malegaon and Samjhauta Express cases – as the main conspirator. Joshi was later murdered, an act allegedly committed by Sadhvi Pragya Singh Thakur.
By 2016, the NIA filed a supplementary chargesheet naming Lokesh Sharma, Dhan Singh, Manohar Singh, and Rajendra Choudhary as the perpetrators who planted the bombs. The agency dropped charges against the original accused, citing a lack of evidence and relying instead on Aseemanand’s confession and new findings.
Court Interventions and Discharges
The NIA’s chargesheet notably criticised previous investigations for focusing disproportionately on the "fake bomb" recovery on September 13 rather than the actual blasts on September 8.
On April 25, 2016, eight of the nine original accused arrested by the ATS were discharged. One of them, Shabbir, passed away while the plea was pending. The ATS and the four accused discharged on Wednesday had filed appeals against that 2016 discharge order, which remain pending before the High Court.
The NIA's case alleged that the four men carried out the blasts under Joshi’s supervision, transporting the bombs from Indore to Malegaon. It claimed the targets were deliberately chosen to spark communal unrest.
However, the four men were granted bail by the High Court on June 14, 2019. The court noted there were no witnesses who saw them planting bombs or purchasing the bicycles used in the attack. The High Court also questioned how bicycle shop owners could reliably identify the men in 2013, seven years after the alleged purchase.
Following the framing of charges by a special court, the four men approached the High Court, which ultimately allowed their appeal and discharged them this Wednesday.
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Timeline of the 2006 Malegaon Blasts Case
• September 8, 2006: Four bombs explode near Hamidia Mosque and Bade Kabristan in Malegaon, killing 31 people and injuring over 100.
• September 13, 2006: A "fake" bomb is discovered on the staircase of the Mohammedia Mosque.
• October 2006: The investigation is officially transferred from local police to the Anti-Terrorism Squad (ATS).
• Late 2006: The ATS arrests nine Muslim men, alleging that members of the banned group SIMI carried out the attacks.
• 2010: Swami Aseemanand is arrested by the CBI and reportedly confesses that a Hindu extremist group was responsible for the blasts.
• 2011: The investigation is transferred to the National Investigation Agency (NIA), leading to a shift in the direction of the probe.
• April 25, 2016: Eight of the nine original accused arrested by the ATS are discharged from the case due to lack of evidence.
• May 2016: The NIA files a supplementary chargesheet naming Lokesh Sharma, Dhan Singh, Manohar Singh, and Rajendra Choudhary as the new accused.
• June 14, 2019: The Bombay High Court grants bail to the four NIA-named accused, citing a lack of witness testimony and reliable identification.
• July 2025: The Bombay High Court acquits two of the original accused in the related 2006 Mumbai train blasts case, criticizing the ATS for using coerced confessions.
• September 30, 2025: A special NIA court frames formal charges against Lokesh Sharma, Dhan Singh, Manohar Singh, and Rajendra Choudhary.
• April 2026 (Wednesday): The Bombay High Court discharges the four NIA-named accused, leaving the 2006 blasts officially unsolved.
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