The Maharashtra Police had announced a probe was under way to establish the cause of the explosion, while a
Central Bureau of Investigation team was sent from
New Delhi to Pune to assist in the investigations. Consequently, the entire country was put on high alert, especially
Mumbai and
Hyderabad. Investigation in the blast was carried out by the Maharashtra government's
Anti Terrorist Squad, along with the
National Investigation Agency in Delhi. Maharashtra ATS Chief K P Raghuvanshi is heading the blast probe. The agency has crucial
closed-circuit television camera (CCTV) footage of the alleged bombers. Investigators first focused their attention on the possibility that the attacks were carried out by a Pune jihad cell known to have existed since at least since 2006. This came out from the questioning of Mohammad Peerbhoy, an Indian Mujahideen operative held in the course of a national counter-terrorism operation that targeted the Lashkar-linked group in 2008. Just moments before the explosion, Paras Rimal, a waiter at the German Bakery had noticed the bag (containing explosives). When Paras moved in to investigate the bag, he was called out of the bakery by an unknown motorist who paid him to fetch a glass of water. Since Paras was away from the blast he sustained mild injuries and has become an important eyewitness for the police. Investigators also included other Indian metropolitan cities like
Bangalore and Mumbai in the probe. Over 40 people were arrested during the investigation, among them four Kashmiris in
Hampi, Karnataka. Pune police arrested two suspects from Pune's suburbs on 16 February 2010. Another two were detained in
Aurangabad. The Maharashtra Anti-Terrorism Squad (ATS) identified
Yasin Bhatkal, believed to be a relative of Indian Mujahideen founder
Riyaz Bhatkal, as one of the main conspirators of the blast in a preliminary report submitted to the State Government on 7 April 2010. The investigating agency, in its report, has identified four more suspects involved in the blast, including the planters of the bomb – laden bag which went off in the German Bakery. Maharashtra home minister
R.R. Patil told the Legislative Council that the suspects would be arrested in a few days and more details would be disclosed at a later stage. On 24 May 2010, Maharashtra ATS arrested Abdul Samad Bhatkal, younger brother of Yaseen Bhatkal, as he got off Air India flight 812 at
Mangalore International Airport for his alleged involvement in a little-known murder case. However, Home Minister
P. Chidambaram later identified him as the prime suspect in the German Bakery blast. Bhatkal had left for Dubai shortly after the blast and was returning after his visa expired. He was arrested using a Lookout Notice that was issued by the Mumbai police. Samad was trying to slip into the country through the Bajpe Airport by taking advantage of the situation that prevailed following the 22 May 2010 crash at Mangalore of flight
Air India Express Flight 812. Bhatkal was apprehended based on investigation of CCTV footage from the German Bakery. On 30 November 2011,
Delhi Police special cell arrested six suspected
Indian Mujahideen operatives whom they claimed to be the perpetrators of the 2010 Pune bombing, the Chinnaswamy stadium blast and the
2010 Jama Masjid attack. One
Pakistani national was also reported to have been arrested. Two of the seven people were arrested in
Chennai and were identified by the special cell as Mohammad Irshad Khan (age 50) and Abdul Rahman (age 19), hailing from
Madhubani district of
Bihar. Another individual – Ghayur Jamil – a student at a
madrasa in
Darbhanga was also arrested from
Madhubani on the charge of recruiting youths from near the Indo-Nepal border for terrorist activities, Abdul Rahman being one of such recruits. This charge was disputed by Jamil's father who billed him as a good orator and an honest, religious man who had lost a bag containing his belongings – including his PAN card, residential proof and photos – a few days back. A Pune court on 18 April 2013 awarded a
death sentence to Indian Mujahideen operative Himayat Baig, who was earlier in the week convicted for his involvement in the blasts. Baig's lawyer A Rahman had said that though they respected the verdict, they would appeal against it in the Bombay High Court. Baig's death sentence was commuted into a life sentence in 2018. == Reaction ==