The ANC's steering committee is currently probing the "disappearance" of 68 delegates' votes following last night's results announcements.
According to News24, a senior ANC delegate has said EleXion Agency -- which conducted the election on the ANC's behalf -- must explain to the ANC what happened to the "missing" votes.
4,776 voting delegates attended conference, but only 4,708 voted.
It is understood this matter is being driven by ANC members who backed Senzo Mchunu to become ANC secretary-general and who are questioning the final voting tally.
Mchunu, the former KwaZulu-Natal ANC chairperson, lost to Free State chair Ace Magashule by 24 votes on Monday night. The position of secretary-general is seen as the engine of Luthuli House.
Magashule received 2,360 votes while Mchunu received 2,336. There were eight abstentions and four spoilt votes.
Supporters said the numbers do not add up, as the EleXion agency announced that 4,708 of 4,776 delegates voted.
"What happened to 68 votes?" one supporter asked via a WhatsApp message.
Another claimed that the steering committee for the 54th ANC national elective conference will be approached to attend to the matter.
On Monday night, a shocked Mchunu was seen going up to the stage and asking to see the final results when Magashule was announced as the winner.
Another source close to Mchunu refused to comment to News24, but said: "Journalists should keep a close eye around developments on the claims throughout the day."
Mchunu was nominated for the position of secretary general on now ANC president Cyril Ramaphosa's slate.
Ramaphosa's faction also lost out on the positions of deputy secretary general and deputy ANC president, with Jessie Duarte retaining her position as deputy secretary general and David Mabuza becoming deputy president.
Meanwhile, ANC head of elections Nomvula Mokonyane has distanced herself from several messages claiming that she tampered with the registration of delegates and the election process.
This was after she was accused of fiddling with the registration process ahead of the conference and asking for a recount of the results after the voting and counting had been completed on Monday.
Voting delegates were 4,776
Ace Magashule got 2,360
Senzo Mchunu got 2,336
There were eight abstentions
There were four spoilt votes
2,360 + 2,336 + 8 + 4 = 4,708
4,776 - 4,708 = 68
Additions and editing by Marc Davies, HuffPost SA.