"Modi-led Hindu fascist regime" is "bulldozing its way into the lives of indigenous adivasis", the letter said.
Pune police intercepted the letter, written on April 18 by "R" addressed to "comrade Prakash".
According to PTI, the police claimed in the sessions court that the letter was found in the premises of Delhi-based activist Rona Wilson's house.
On Wednesday, 5 people were arrested in connection with the Bhima-Koregaon caste violence in January. Dalit activist Sudhir Dhawale, lawyer Surendra Gadling, activists Mahesh Raut and Shoma Sen and Rona Wilson are alleged to have ties with banned CPI-Maoists.
The letter spoke euphorically about creating "another Rajiv Gandhi like incident" and also explained the urgent need of 8 crore rupees for obtaining M-4 rifle and four lakh rounds.
"The message does not explicitly say the plan is to assassinate Modi, but its implication is clear", public prosecutor Ujjwala Pawar told the court.
A copy of the letter, released by ANI news agency, says: "...inspite of big defeats like Bihar and West Bengal, Modi has successfully established BJP governments in more than 15 states. If this pace continues then it would mean immense trouble for the party on all fronts...Col Kisan and a few other senior comrades have proposed concrete steps to end the Modi-era."