With this, the number of accused arrested in the Pansare case has gone up to 12.
The trio -- Sachin Andure, Amit Baddi and Ganesh Miskin -- was lodged in jails in Mumbai and Pune under judicial custody in different cases, they said.
The suspects were formally arrested from jails in the Pansare case by the SIT of the state CID, the officials said.
Andure, an alleged sharp shooter, was lodged in Pune's Yerawada Jail in the Narendra Dabholkar case, while Baddi and Miskin were under judicial custody in Arthur Road jail of Mumbai, they said.
Baddi and Miskin are accused in the Gauri Lankesh case of Karnatka and also in the Nallasopara arms haul case of Maharashtra.
Pansare was shot at on February 16, 2015, in Kolhapur and succumbed to his injuries on February 20.
Narendra Dabholkar, a noted rationalist, was shot dead on August 20, 2013, in Pune while he was on a morning walk.
Gauri Lankesh, an activist-journalist, was shot dead on the night of September 5, 2017, from a close range in front of her Rajarajeshwari Nagar house in Bengaluru.
Security agencies suspect all three murders are interlinked and carried out by the same set of people.
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