The Maharashtra Anti-Terrorism Squad (ATS) initially blamed the bombings on the Students Islamic Movement of India (SIMI), but in a chargesheet filed in 2013 the NIA and ATS (Anti-Terrorism Squad) joint investigation and involved evidences pointed towards the involvement of eight members of jihadi extremist group claiming to be from Abhinav Bharat, who were later released from charges due to lack of evidence.

On 11 September, Maharashtra Director General of Police P. S. Pasricha said that the officers investigating the blasts had produced leads and expressed confidence that a breakthrough would be achieved soon.

[21] On 10 September, police sources said that the methods used are similar to attacks on mosques earlier in 2006 for which 16 innocent Hindu activists were arrested.

[23] Malegaon has been the focus of communal tension for some time,[clarification needed] which spilled out into the open in 1984, 1992, and 2001, when there were large scale protests over the United States invasion of Afghanistan.

[9] In May 2006, police recovered a cache of RDX explosives and automatic rifles from the region based on information they said was provided by arrested extremist Islamists.

Since the investigation was still under way, Nasik Superintendent of Police Rajvardhan declined to give details, saying: "We can't say anything till we get reports from all the agencies".

The Anti-Terrorism Squad probing into the case has already arrested eight suspects, including two booked in the 11 July Mumbai serial blasts, in connection with four explosions that rocked the town killing 31 people and injuring more than 200.

Seeking their remand, public prosecutor Raja Thakre said the accused had played a vital role in the conspiracy and investigations conducted by Anti-Terrorist Squad so far had revealed involvement of more persons who are yet to be arrested.

[39][40] On 7 May 2024, the National Investigation Agency (NIA) said the says Maharashtra Anti Terrorist Squad (ATS) planted RDX to frame Shrikant Purohit and many others, who were tortured to take names of Hindu leaders.