According to the Sunday Times Motlanthe was nominated by branch 42 in Boksburg, whose membership includes ANC secretary-general Gwede Mantashe. He received an "overwhelming" 90 votes to Zuma's seven, according to the weekly.
Cape Town's Gaby Shapiro branch also chose Motlanthe.
SA Communist Party deputy general secretary Jeremy Cronin, who is also public works deputy minister, belongs to the branch, as does Tourism Minister Marthinus van Schalkwyk.
Both left the meeting shortly before nominations began, the paper reported.
Earlier this year Motlanthe reaffirmed the primacy of ANC branches in electing the party's leadership.
"His position is clear. Leaders must respect the right of branches to elect leaders," said Motlanthe's spokesperson Thabo Masebe.
"Nothing must be done to take away that right."
When leaders aligned themselves with particular factions, or canvassed support, it led to divisions within the ruling party.
"Once they [leaders] get involved in any discussions, it means they have already decided they want leadership positions."
Masebe was speaking after the Sunday Times reported that Motlanthe had rejected overtures from a Zuma-aligned lobby group which wanted to cut a deal for the party's leadership.
Many in the ruling party are said to favour Motlanthe as the party's next leader over President Jacob Zuma.
Winnie Madikizela-Mandela attacked Zuma in an MTV interview in September, the paper reported earlier this year.
It was difficult to promote a single sexual partner to young people when the president had multiple partners, she reportedly said.
"People have to redefine an acceptable culture that is going to define you as an African and, at the same time, retain your dignity as an African," the Sunday Times quoted her as saying.
She also hinted she was opposed to the Protection of State Information Bill.
"I'm sure you would know what I would think about that [Bill]," she reportedly said, noting that ANC MP Ben Turok had abstained from voting on the Bill and was facing disciplinary action as a result.
The ANC in the Western Cape was also concerned that too many of its branches have been disqualified after an audit ahead of the Mangaung conference.
ANC members claim that an unusually large number of branches in the province have failed to meet requirements to attend the conference.
They blame auditors for discriminating against branches in the Western Cape and disqualifying them over minor issues. Other members have laid the blame with the current provincial leadership, accusing it of failing to build branches.
The number of branches each province takes to Mangaung will be crucial for votes at the December conference, at which a leadership contest is expected.
A senior provincial leader told the Mail & Guardian that just less than 180 of the province's 274 branches are in good standing. Initially only 126 had qualified, but the number improved after mistakes were corrected.
A senior ANC official in the Southern Cape region said that initially only 10 of the region's 51 branches had qualified, but the number had increased to 29.
The official, who was not authorised to comment officially, dismissed claims that auditors were unfair and said the regional and provincial leadership had failed to build branches.
"That the auditors were harsh is nonsense," he said.
For a branch to be in good standing, it must have at least 100 members, hold branch meetings with a proper quorum and be able to show that membership forms have been completed.
"Branches are given a chance to fix these things, but some of the things can't be fixed – like quorums or forms that have not been signed or are without ID numbers. It's a weakness of regional and provincial leadership, because the ANC informed people of what was needed to be done as far back as January.
"You should do your own verification; pick up those things before the cut-off date. But some branches have not had meetings since last year," said the official, who said he supported President Jacob Zuma's re-election in Mangaung.
An ANC member from Worcester in the Boland, who preferred to remain anonymous, said many branches had been disqualified in the region because they had submitted information without supporting documents.
The member, who is opposed to Zuma's re-election, said the auditors should have been more flexible in these cases. He alleged that auditors had sidelined the branches and regions that were perceived to be opposed to Zuma.
A senior provincial leader agreed with those who questioned the auditors, saying the auditing process had been "extremely subjective".
Not a foolproof process
"In some instances, they'll say 'okay, fix the problem' but other times they'll just say no."
"It's not a foolproof process. Even the SG [secretary general Gwede Mantashe] cannot vouch for it."
The leader also felt that the auditing team had acted harshly in disqualifying many Western Cape branches. He claimed that Mantashe, whom the ANC youth league wants removed from his position at the Mangaung conference, handpicks the auditing teams – which are composed of ANC members.
"If they [auditors] carry a particular mandate, they audit that way, disqualifying branches over minor issues. In provinces where they think the leadership is calling for change [of national leadership], they are harsh."
Provincial secretary Songezo Mjongile refused to confirm or deny the allegations. He said it was premature to comment on the audits because Mantashe had not signed off the results. He was supposed to do this at the special national executive committee meeting, which was expected to take place on September 28, but the date had not been confirmed at the time of going to press.
Mjongile said he was concerned about branches not taking their work seriously. "People should have programmes of action to ensure that branches are in good standing and don't just exist for conferences," he said.