Prakash Ambedkar, the grandson of Dalit icon B R Ambedkar, said Maharashtra Democratic Front, Maharashtra Left Front, besides 250 organisations, have supported Wednesday's shutdown.
A senior police official, however, said Monday the charges against the 85-year-old in the Koregaon-Bhima violence case have not been dropped.
Ekbote was arrested soon after the Supreme Court turned down his anticipatory bail plea earlier in the day, the official added.
The protesters blocked roads in several areas of Mumbai, forced shops to shut down.
The Union home ministry has received a factual report from the Maharashtra government on the prevailing situation in the state in the wake of caste-based violence there, a ministry spokesperson said.
Bharadwaj claimed a number of human rights lawyers, activists and organisations were deliberately named to cast a stigma over them, obstruct their work and incite hatred against them.