The SIT has summoned the district president of fringe right-wing outfit Sri Ram Sene.
The official said the organisation, composed of people drawn from Hindu right groups, had around 60 members spread across at least five states but had no name.
The two -- Amit Raghavendra Baddi and Ganesh Miski -- both residents of Hubballi, were arrested on Sunday, special investigating officer M N Anucheth said.
The film and theatre personality was among the most vocal critics of hardline Hindutva whose security was beefed up following the killing of Lankesh in September last year.
Rushikesh Devdikar alias Murali, 44, who was absconding was arrested on Thursday from his hideout at Katras in Dhanbad district of Jharkhand, the SIT said in a statement. According to the probe team, Devdikar was part of the conspiracy to kill Lankesh. He is accused number 18 in the case.
An SIT officer probing the murder case said the investigation is in final stage and a chargesheet will be filed in two months.
In August 2016, at a meeting of the syndicate, the main members identified Lankesh as a durjan "as told in the Kshatra Dharma Sadhana based on her speeches and writings
'Why she was killed? Because she believed in a certain ideology, she wrote and spoke on that'
"No one questioned the Congress government's failure. Instead, they are asking why is Prime Minister (Narendra) Modi silent and not speaking on Gauri Lankesh's death. Many wanted PM Modi to react after Gauri Lankesh's death. Why should Modi react if some dog dies in Karnataka?"