As news of Rana's arrest spread, several of his supporters reached the Gomtinagar police station and tried to prevent police from taking him away to an undisclosed destination.
Similar arrest warrants have been issued against 16 political leaders including four BJP legislators, a Congress leader and a Bahujan Samaj Party MP.
All of them have been accused of inciting people in Muzaffarnagar, where communal violence this month left more than 40 people dead and thousands displaced.
Laxmikant Bajpayi, the Uttar Pradesh BJP president, told IANS that the party will defend its leaders in courts.
He accused the Samajwadi Party government of acting against BJP leaders without proof and in order to "appease the minority community".