Delegates at the provincial general council had cast their votes for the ANC's top six in a secret ballot, and counting began just before 5am on Thursday.
It appears some of the disputes from ANC members – who claimed the selection of delegates was done fraudulently – were still underway.
On Wednesday night, a brief fracas erupted outside the Cape Peninsula University of Technology hall where the council was being held.
A group of members from ANC branches in the Boland region demanded access to the council to settle disputes about the selection of branch delegates.
A woman from the New Rest branch in Wellington, Primrose Mbenene, told the South African Press Association she and some fellow supporters were "robbed" of having a say on who their branch delegate for the council should be.
She insisted she and fellow branch members were being sidelined because they supported Kgalema Motlanthe to replace Jacob Zuma as ANC president at Mangaung.
Mbenene said over the past few weeks several branch meetings were postponed because they didn't have a quorum.
"They then take out people to a shebeen to have a meeting," she said.
She said they lodged five complaints over the election of their branch delegates to the ANC's provincial office and had yet to get a response.
Another woman, claiming to be the deputy chairperson of the ward seven branch in Wellington, Elsie Magoda, said she was originally meant to be a delegate.
Magoda alleges the chairperson of her branch made members sign for another delegate "in the middle of the night".
"I was a delegate but they stole it from me. It's fraud," she said.
Members of the ANC's national executive committee (NEC) task team arrived in Cape Town on Wednesday afternoon to hear and rule on disputes.
NEC members present included Public Service and Administration Minister Lindiwe Sisulu, Health Minister Aaron Motsoaledi, Communications Minister Dina Pule and Gauteng Premier Nomvula Mokonyane.
Struggle stalwart Andrew Mlangeni, of the ANC electoral commission, was also in attendance.
Delegates were expected to conclude their nominations for the 80 member ANC NEC, before announcing the results of the top six vote.
Divisions remained evident at the PGC with some branch delegates singing pro-Zuma songs, while others chanted the word "change" several times.
The latter wanted to see a change in leadership, insisting Motlanthe should replace Zuma at the party's elective conference which is due to start in Mangaung on December 16. – Sapa