Ndii had been arrested over suspected meeting with MRC.
Police held him overnight, transferring him to Nairobi where he was then released on Sh10, 000 bond.
Ndii has recently called for secession along NASA strongholds while MRC has called for the secession of the Coast from Kenya.
MRC deputy spokesperson, Richard Lewa, said the arrest was an attempt to crack down MRC members.
"We are law-abiding people and will not be lured into any trap. We have no association with Ndii, neither do we have any association with NASA, Jubilee or any other political outfit," Lewa told The Star.
MRC Council of Elders secretary James Malembi accused the government of wanting to drag other people in its political war against NASA.
“We have said several times that MRC is not affiliated to any political outfit. We are independent and we are seeking secession through legal means,” Lewa said