[14] In August 2010, security analyst Bahukutumbi Raman questioned "the two different versions that have emerged from Indian and American investigators.

[18] On 19 November 2010, the CBI produced the preacher Swami Aseemanand before the court in connection with the Makkah Masjid blast in Hyderabad in May 2007.

[19][20][21][22] On 18 December, he confessed in front of a magistrate, citing the guilt he felt after seeing innocent Muslim boys arrested in the case by the police.

[24] The Anti Terrorist Squad (India) (ATS) and CBI subsequently questioned former members of the RSS,[25][26][27][28][29][30] and in December 2010 charged Aseemanand as the mastermind behind the Makkah Masjid bombing.

The letter, which was never sent, was addressed to the presidents of India and Pakistan and explained why he had wanted to confess and tell the truth after seeing the innocent people that had been arrested and implicated with him.

[35] The letter confession of the prompted families of the 32 men arrested in the aftermath of the bombing demanded the release of the youths from jail.

[29][43] In January 2013, the then Indian Home Minister Sushilkumar Shinde, of Indian National Congress, accused Rashtriya Swayamsevak Sangh and Bharatiya Janata Party for setting up camps to train terrorists, and alleged involvement in planting bombs in the 2007 Samjhauta Express bombings, Mecca Masjid blast and 2006 Malegaon blasts.

[44] Rashtriya Swayamsevak Sangh spokesperson Ram Madhav responded to this allegation by accusing Shinde of pandering to Islamist groups like Jamaat-ud-Dawah and Lashkar-e-Taiba.

[46] In September 2013, Yasin Bhatkal confessed that Indian Mujahideen had bombed two other places in Hyderabad later in August 2007 to avenge Mecca Masjid blast which was then allegedly attributed to Hindu fundamental groups.