Ivanovic tendered his resignation at an HNV session in Subotica, northern Serbia, after his motion to dismiss HNV executive committee chairman Laza Vojnic did not receive the sufficient number of votes.
Ivanovic said he wanted Vojnic to be replaced because oversights in performance prevented the HNV from acting more effectively.
Vojnic said the vote in his favour meant that the accusations against him were unfounded.
Two HNV vice presidents, its secretary and one member of the executive committee resigned as well.