The ANC's OR Tambo region has reelected Thandekile Sabisa as chairperson.
Sabisa is said to be pushing for a change in the national leadership.
The anti-Zuma faction in the Eastern Cape believe Zuma has marginalised senior ANC leaders in the province since he took over as president in 2009. They complain that Zuma has removed several ministers from his Cabinet and senior government officials from the Eastern Cape and replaced them with those who hail from KwaZulu-Natal, his home province.
OR Tambo is the party's second largest region after eThekwini in KwaZulu-Natal, and constitutes about 70% of the Eastern Cape delegates who will participate in the national conference in Mangaung at the end of the year.
Voting had begun after 5am on Sunday for the top five positions within the regional executive committee, said ANC Eastern Cape chairperson Pumulo Masualle.
ANC leaders in the Eastern Cape took control of the region earlier this month after its regional conference was adjourned before new leaders could be elected.
There were allegations that membership figures were inflated, and that there were several "ghost" delegates.
The ANC leaders — including ANC secretary general Gwede Mantashe — ealier ruled the regional executive committee must reconvene the conference this weekend.
The decision by the ANC's top six to intervene was seen as an indictment of the Eastern Cape's provincial leaders. They stand accused of having been at the centre of the chaotic gathering that came to an abrupt end after members of the provincial executive committee (PEC) decided to dissolve the conference and withhold the results.
The electoral commission at the conference discovered that votes were cast by 591 delegates, instead of the 587 adopted by the plenary. The PEC adjourned the conference afterwards.
Sabisa is seen as among those pushing for what has become known as the "anyone but Zuma" faction when the party meets in Mangaung.