Hari Sauri das spokesman for ISKCON Mayapur said Sripada Maharaja had been receiving treatment for an injury he sustained in a grenade attack at Janmastami in ISKCON's Manipur temple on August 16, 2006, during the Janmastami celebrations. Six devotees including two children were killed and over 40 devotees were seriously injured. Sripada Maharaja had a deep cut and a fractured bone in his left forearm, a small puncture in his left eardrum and a shrapnel burn on his back. He was admitted to the Apollo Hospital where he underwent successful operations on his forearm and ear. Ten days later a routine checkup revealed the burn on his back had almost healed, and doctors were surprised by how quickly the fractured bone in his forearm was setting.

Sripada Maharaja's body was taken to Krishna Balaram temple in Vrindavan Dham where many devotees had his darshan before the Samadhi ceremony on October 4, 2006, the disappearance day of Srila Raghunathadas Goswami and Srila Raghunatha Bhatta Goswami. Srila Krishnadas Kaviraja Goswami appeared on this day also. Sripada Maharaja's desire, was to be placed in Samadhi at the Gopaldeva Mandir on the banks of Radhakunda.

Sripada Maharaja was well known for his unwillingness to compromise on Srila Prabhupada's instructions, and a book called “Bhagavata Sevarpanam” about Sripada Maharaja’s service to Srila Prabhupada is available from the Bhaktivedanta Institute, Calcutta.