Several Trinamool Congress leaders were detained after they started a 24-hour protest outside the Election Commission office in Delhi on April 8.
The party is demanding that the chiefs of CBI, NIA, ED and Income Tax Department be changed.
A delegation of the TMC leaders, including Derek O'Brien, Dola Sen, Saket Gokhale and Sagarika Ghose met a full bench of the Election Commission over their demands.
The TMC has alleged that the central probe agencies have been targeting opposition parties at the behest of the BJP-led Centre.
"The BJP is misusing central agencies against us. The way NIA, ED and CBI are working and targeting TMC leaders is shameful. We would request the EC to ensure a level playing field for all political parties," Sen told reporters at the Kolkata airport before leaving for New Delhi.
The TMC alleged on Sunday an "unholy alliance" between the NIA and the BJP ahead of elections, prompting the central investigating agency to deny any mala fide intention and label the entire controversy as "unfortunate".
A team of the NIA was allegedly attacked by a mob on Saturday when it went to arrest two main suspects in a 2022 blast case in West Bengal's Purba Medinipur district, sparking a political slugfest with Chief Minister Mamata Banerjee accusing the investigators of assaulting the villagers.