According to Sanstha spokesperson Chetan Rajhans, the letter also mentioned that women inmates of the ashram, located at Ramnathi near Ponda town, around 40 kms from here, will be assaulted.
The single-page letter, typed in English, has been sent from Bengaluru.
"The letter which claims to be written by one Jamesh Annamalai was received at 10.30 AM today through post," Rajhans told PTI.
The letter, addressed to Rajhans, threatens to eliminate Athavale, who lives in the ashram, as well as the women inmates.
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The Ponda Police have confirmed receipt of the complaint.
"We have received the application seeking registration of an offence. We will investigate the matter," Ponda Police Inspector Harish Madkaikar said.
The Sanstha has been under scanner in connection with the killing of Maharashtra rationalist Narendra Dabholkar.
The CBI had arrested Sanstha member Virendra Tawde from Maharashtra in the Dabholkar murder case last year.
The Maharashtra Police had also questioned Tawde in connection with the 2015 killing of CPI leader and rationalist Govind Pansare.